From 56b23269563c8442fb0b72e551536553e453dd07 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Mon, 9 Sep 2024 07:47:59 +0000
Subject: [PATCH] Update latest documentation

---
 latest/examples/gwas_tutorial.html            | 540 +++++++++---------
 latest/examples/relatedness_tutorial.html     |  52 +-
 .../sgkit.variables.call_dosage_spec.html     |   2 +-
 ...t.variables.interval_contig_name_spec.html |   2 +-
 .../sgkit.variables.parent_id_spec.html       |   2 +-
 .../sgkit.variables.sample_id_spec.html       |   2 +-
 .../sgkit.variables.traits_spec.html          |   2 +-
 .../sgkit.variables.variant_contig_spec.html  |   2 +-
 ...variables.variant_genotype_count_spec.html |   2 +-
 .../sgkit.variables.variant_id_spec.html      |   2 +-
 latest/searchindex.js                         |   2 +-
 latest/user_guide.html                        |   4 +-
 12 files changed, 307 insertions(+), 307 deletions(-)

diff --git a/latest/examples/gwas_tutorial.html b/latest/examples/gwas_tutorial.html
index 20e53692e..3e12c1fc0 100644
--- a/latest/examples/gwas_tutorial.html
+++ b/latest/examples/gwas_tutorial.html
@@ -610,7 +610,7 @@ <h2>Importing data from VCF<a class="headerlink" href="#importing-data-from-vcf"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2751/2446290678.py:1: DeprecationWarning: Functions for reading VCF are deprecated, please use the bio2zarr package.
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2652/2446290678.py:1: DeprecationWarning: Functions for reading VCF are deprecated, please use the bio2zarr package.
   vcf_to_zarr(&quot;1kg.vcf.bgz&quot;, &quot;1kg.zarr&quot;, max_alt_alleles=1,
 [W::bcf_hdr_check_sanity] PL should be declared as Number=G
 </pre></div>
@@ -1021,7 +1021,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
     variant_id_mask       (variants) bool 11kB dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;
     variant_position      (variants) int32 44kB dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;
     variant_quality       (variants) float32 44kB dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;
-Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-ef6ad097-a7cc-4a1c-b8e6-d7e6631e9b74' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-ef6ad097-a7cc-4a1c-b8e6-d7e6631e9b74' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span>samples</span>: 284</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-9e2e9fc1-3771-4c87-a8f3-d14ad65ce325' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-9e2e9fc1-3771-4c87-a8f3-d14ad65ce325' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-6ea4451a-0e4c-4079-ba0d-115807d68d1e' class='xr-section-summary-in' type='checkbox'  checked><label for='section-6ea4451a-0e4c-4079-ba0d-115807d68d1e' class='xr-section-summary' >Data variables: <span>(17)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-3f9fb553-0d01-4b04-95c9-0140fc58e073' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3f9fb553-0d01-4b04-95c9-0140fc58e073' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-52213f07-2375-4343-8610-298e207037bc' class='xr-var-data-in' type='checkbox'><label for='data-52213f07-2375-4343-8610-298e207037bc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-39d51e0b-7a2f-4e2c-bb13-c0a6c0bdddff' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-39d51e0b-7a2f-4e2c-bb13-c0a6c0bdddff' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span>samples</span>: 284</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-c9f32473-e5cc-43b8-8670-5d282006da36' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c9f32473-e5cc-43b8-8670-5d282006da36' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-fa45095f-f355-45b6-8847-cb125e61bf51' class='xr-section-summary-in' type='checkbox'  checked><label for='section-fa45095f-f355-45b6-8847-cb125e61bf51' class='xr-section-summary' >Data variables: <span>(17)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-15c7e9b3-e36b-40f5-908d-64f25ed6f047' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-15c7e9b3-e36b-40f5-908d-64f25ed6f047' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-24abb2ca-dabc-4158-b4f7-4826d0953cd4' class='xr-var-data-in' type='checkbox'><label for='data-24abb2ca-dabc-4158-b4f7-4826d0953cd4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1101,7 +1101,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-a771ea5c-97ac-46d8-9517-9fa5c6b51b70' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a771ea5c-97ac-46d8-9517-9fa5c6b51b70' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e3105457-d7e9-4b6e-9cb5-fd9810e0cdc9' class='xr-var-data-in' type='checkbox'><label for='data-e3105457-d7e9-4b6e-9cb5-fd9810e0cdc9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-163b1849-5e3c-4119-8a1e-2234e83264e1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-163b1849-5e3c-4119-8a1e-2234e83264e1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cbca36cf-c7ef-4ef8-99e0-6ab9dddf1660' class='xr-var-data-in' type='checkbox'><label for='data-cbca36cf-c7ef-4ef8-99e0-6ab9dddf1660' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1157,7 +1157,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-930ed4c0-42df-475d-94ab-e707c45dfe1b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-930ed4c0-42df-475d-94ab-e707c45dfe1b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a3d19691-a4bc-4a88-8e28-ac321648ca36' class='xr-var-data-in' type='checkbox'><label for='data-a3d19691-a4bc-4a88-8e28-ac321648ca36' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-fb75bd5b-562f-4645-84ce-fcdba91c5e1b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fb75bd5b-562f-4645-84ce-fcdba91c5e1b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-53599e2f-5a44-4f2a-b727-99a90b2d489b' class='xr-var-data-in' type='checkbox'><label for='data-53599e2f-5a44-4f2a-b727-99a90b2d489b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1213,7 +1213,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-c05de523-7244-4c00-ad77-16448b7df9c4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c05de523-7244-4c00-ad77-16448b7df9c4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2e12a49f-3ca7-453a-908e-5a94073a214b' class='xr-var-data-in' type='checkbox'><label for='data-2e12a49f-3ca7-453a-908e-5a94073a214b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-753038cb-b7d8-4154-a91f-eb2186620a78' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-753038cb-b7d8-4154-a91f-eb2186620a78' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-62a2ec20-50d2-4f6c-ae45-8c2b6739a55d' class='xr-var-data-in' type='checkbox'><label for='data-62a2ec20-50d2-4f6c-ae45-8c2b6739a55d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
 the first allele, 2 for the second allele), -1 to indicate a
 missing value, or -2 to indicate a non allele in mixed ploidy datasets.</dd><dt><span>mixed_ploidy :</span></dt><dd>False</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -1295,7 +1295,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-6725102c-7153-4f0a-a2bf-ad4c40e01838' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6725102c-7153-4f0a-a2bf-ad4c40e01838' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-84185505-e59e-461c-9e0a-33d537401c8d' class='xr-var-data-in' type='checkbox'><label for='data-84185505-e59e-461c-9e0a-33d537401c8d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-8382925e-de89-4102-a44a-15174ba90174' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8382925e-de89-4102-a44a-15174ba90174' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-81d91194-3a10-4482-a1e6-9e0bb62a9b87' class='xr-var-data-in' type='checkbox'><label for='data-81d91194-3a10-4482-a1e6-9e0bb62a9b87' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1375,7 +1375,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-c03f1a99-c793-406e-b068-d4acd5e6bb80' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c03f1a99-c793-406e-b068-d4acd5e6bb80' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8a342d61-0b3f-473c-bd6b-0ec6b8bbd4f4' class='xr-var-data-in' type='checkbox'><label for='data-8a342d61-0b3f-473c-bd6b-0ec6b8bbd4f4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-76ad89da-adea-4a9f-88f5-0b91c1356842' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-76ad89da-adea-4a9f-88f5-0b91c1356842' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7c9d21c9-7c4c-4019-b719-ebc31fa934e6' class='xr-var-data-in' type='checkbox'><label for='data-7c9d21c9-7c4c-4019-b719-ebc31fa934e6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
 all calls are unphased.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -1432,7 +1432,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-9cf5326f-1c5a-483a-b0b8-f85af34a02f5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9cf5326f-1c5a-483a-b0b8-f85af34a02f5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f7139175-1487-435e-84f4-28bd953243fd' class='xr-var-data-in' type='checkbox'><label for='data-f7139175-1487-435e-84f4-28bd953243fd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-fedb8599-121d-4732-87a3-3209c361b81a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-fedb8599-121d-4732-87a3-3209c361b81a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-df677fd6-7147-43e9-872c-40083da15940' class='xr-var-data-in' type='checkbox'><label for='data-df677fd6-7147-43e9-872c-40083da15940' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1487,7 +1487,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-a5c90070-eecd-42ee-b9ff-7947d5640a53' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a5c90070-eecd-42ee-b9ff-7947d5640a53' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c6a23f82-eac9-4710-85fe-38a78fe99b23' class='xr-var-data-in' type='checkbox'><label for='data-c6a23f82-eac9-4710-85fe-38a78fe99b23' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-c7ad92b2-121f-4e16-a45b-a83e13d9033c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c7ad92b2-121f-4e16-a45b-a83e13d9033c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4ef6d205-7aed-4b9e-8594-6e2b457a1776' class='xr-var-data-in' type='checkbox'><label for='data-4ef6d205-7aed-4b9e-8594-6e2b457a1776' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1542,7 +1542,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-d1881bf0-8336-41f5-b580-d9e4545eadce' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d1881bf0-8336-41f5-b580-d9e4545eadce' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fceca2b1-ad9d-43cc-9a55-7f6efd1b53a1' class='xr-var-data-in' type='checkbox'><label for='data-fceca2b1-ad9d-43cc-9a55-7f6efd1b53a1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-8961ad6f-4308-4fdc-9bcf-6a68c4140289' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8961ad6f-4308-4fdc-9bcf-6a68c4140289' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cef9e35b-efdd-4903-aa38-383ed3f6bc41' class='xr-var-data-in' type='checkbox'><label for='data-cef9e35b-efdd-4903-aa38-383ed3f6bc41' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1597,7 +1597,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-cfed6583-de70-40ff-a08b-eed4378bcf8e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cfed6583-de70-40ff-a08b-eed4378bcf8e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-35233aba-e35f-477d-b7fd-de794dba2892' class='xr-var-data-in' type='checkbox'><label for='data-35233aba-e35f-477d-b7fd-de794dba2892' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the sample.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-3cb7eb96-59d1-4c0f-844f-849e3bbacc3d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3cb7eb96-59d1-4c0f-844f-849e3bbacc3d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6703ca72-c90d-4625-9bf7-52626cb8e930' class='xr-var-data-in' type='checkbox'><label for='data-6703ca72-c90d-4625-9bf7-52626cb8e930' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the sample.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1652,7 +1652,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-b40eeeef-85e5-4375-bdb5-d993059152fb' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b40eeeef-85e5-4375-bdb5-d993059152fb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-59f59b68-1220-403e-a33d-0c911bf3c613' class='xr-var-data-in' type='checkbox'><label for='data-59f59b68-1220-403e-a33d-0c911bf3c613' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-df80e141-0a0a-4b97-a8dc-64b7fe15f786' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-df80e141-0a0a-4b97-a8dc-64b7fe15f786' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dbf183c0-f4b2-45fc-a7ac-bc2a33447b78' class='xr-var-data-in' type='checkbox'><label for='data-dbf183c0-f4b2-45fc-a7ac-bc2a33447b78' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1708,7 +1708,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-8cf6306b-410c-4124-b769-6ab0dbf7f887' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8cf6306b-410c-4124-b769-6ab0dbf7f887' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5bac8afd-21ab-4d25-bc34-76b3a9df0f6e' class='xr-var-data-in' type='checkbox'><label for='data-5bac8afd-21ab-4d25-bc34-76b3a9df0f6e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-44e976b3-393e-48a5-be21-6e9f3986d392' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-44e976b3-393e-48a5-be21-6e9f3986d392' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1a827931-6971-48c3-a5e3-4b2e6d3db479' class='xr-var-data-in' type='checkbox'><label for='data-1a827931-6971-48c3-a5e3-4b2e6d3db479' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -1766,7 +1766,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-d65ab29e-441f-4d7f-9695-b963bab4b061' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d65ab29e-441f-4d7f-9695-b963bab4b061' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d0d8235c-89c5-48b4-8010-e6d1e46d252b' class='xr-var-data-in' type='checkbox'><label for='data-d0d8235c-89c5-48b4-8010-e6d1e46d252b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-e35ca06a-2676-4531-9153-cd6ddfcf809e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e35ca06a-2676-4531-9153-cd6ddfcf809e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d03b538c-74b2-4ee4-8490-d5c0bdc1025d' class='xr-var-data-in' type='checkbox'><label for='data-d03b538c-74b2-4ee4-8490-d5c0bdc1025d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1822,7 +1822,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b4e5e45e-2b6d-4f0f-a1b9-6a410bc5a80a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b4e5e45e-2b6d-4f0f-a1b9-6a410bc5a80a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-977df935-497e-486d-b69e-23c3d9cf0d26' class='xr-var-data-in' type='checkbox'><label for='data-977df935-497e-486d-b69e-23c3d9cf0d26' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-8987f7e2-b796-4185-9cbb-6e9d0693d28e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8987f7e2-b796-4185-9cbb-6e9d0693d28e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6264fbb1-1fd1-49a0-93d8-ce3c8fe7c1d1' class='xr-var-data-in' type='checkbox'><label for='data-6264fbb1-1fd1-49a0-93d8-ce3c8fe7c1d1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1878,7 +1878,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-7fa8d1f5-84df-4089-a1ab-1208ceb93295' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7fa8d1f5-84df-4089-a1ab-1208ceb93295' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6c3fbca6-e2ba-4c46-a5d7-e7cdb6a5082c' class='xr-var-data-in' type='checkbox'><label for='data-6c3fbca6-e2ba-4c46-a5d7-e7cdb6a5082c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-a2e8e823-b8ee-44fc-9442-8cc12d314f0d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a2e8e823-b8ee-44fc-9442-8cc12d314f0d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-13c44472-3e9b-45a7-a733-5a7d0b16702c' class='xr-var-data-in' type='checkbox'><label for='data-13c44472-3e9b-45a7-a733-5a7d0b16702c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1934,7 +1934,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d26ada19-1750-4a1a-b30e-b61c383dd18f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d26ada19-1750-4a1a-b30e-b61c383dd18f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-45e859cb-d2bf-4284-aa54-008b5598caa4' class='xr-var-data-in' type='checkbox'><label for='data-45e859cb-d2bf-4284-aa54-008b5598caa4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-7c877c26-eb2b-4d9f-8beb-3a540c48042e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7c877c26-eb2b-4d9f-8beb-3a540c48042e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-64f3504c-209e-4d55-87e7-425e8bd96e74' class='xr-var-data-in' type='checkbox'><label for='data-64f3504c-209e-4d55-87e7-425e8bd96e74' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -1990,7 +1990,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-f74d6cfd-9531-4c40-b75b-738a1cace692' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f74d6cfd-9531-4c40-b75b-738a1cace692' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-23c1c147-2497-48a0-9d76-29cb15ece50f' class='xr-var-data-in' type='checkbox'><label for='data-23c1c147-2497-48a0-9d76-29cb15ece50f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-06de0ea8-49f7-4731-9c55-951a63f84022' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-06de0ea8-49f7-4731-9c55-951a63f84022' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d6a5279b-b625-4809-af50-eff653324afa' class='xr-var-data-in' type='checkbox'><label for='data-d6a5279b-b625-4809-af50-eff653324afa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -2046,7 +2046,7 @@ <h2>Getting to know our data<a class="headerlink" href="#getting-to-know-our-dat
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-ad7a78c0-50ba-408f-a12c-638d10e99996' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-ad7a78c0-50ba-408f-a12c-638d10e99996' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-b0c464a5-4ab7-450a-98f8-bf45c54e4487' class='xr-section-summary-in' type='checkbox'  ><label for='section-b0c464a5-4ab7-450a-98f8-bf45c54e4487' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-4243f5c9-0dc8-4585-8d72-23108675968d' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-4243f5c9-0dc8-4585-8d72-23108675968d' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-c6553d85-d317-4b99-a490-0c0b23397e1b' class='xr-section-summary-in' type='checkbox'  ><label for='section-c6553d85-d317-4b99-a490-0c0b23397e1b' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -2945,7 +2945,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
     isFemale              (samples) bool 284B False True False ... False True
     PurpleHair            (samples) bool 284B False False False ... True True
     CaffeineConsumption   (samples) int64 2kB 4 4 4 3 6 2 4 2 ... 6 4 6 4 6 5 5
-Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-b1f4d26b-da45-41c4-8f09-04b01aed0b05' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-b1f4d26b-da45-41c4-8f09-04b01aed0b05' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-24e00611-a65e-409b-82de-f1edb3dddf80' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-24e00611-a65e-409b-82de-f1edb3dddf80' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-732ed7dd-7482-4f70-983b-837342a12c65' class='xr-section-summary-in' type='checkbox'  checked><label for='section-732ed7dd-7482-4f70-983b-837342a12c65' class='xr-section-summary' >Data variables: <span>(22)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-1921af80-5ea0-4376-a2a6-46dd784d0089' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1921af80-5ea0-4376-a2a6-46dd784d0089' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fde61e92-20a3-444a-9eb3-e85060b595aa' class='xr-var-data-in' type='checkbox'><label for='data-fde61e92-20a3-444a-9eb3-e85060b595aa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-6a199d2d-f3c5-42a1-8b21-77d5d158832c' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-6a199d2d-f3c5-42a1-8b21-77d5d158832c' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-8267cd45-3882-43ec-8f85-e0209f52d806' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-8267cd45-3882-43ec-8f85-e0209f52d806' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-cb45a12e-42e2-4230-9df1-b470cf290dda' class='xr-section-summary-in' type='checkbox'  checked><label for='section-cb45a12e-42e2-4230-9df1-b470cf290dda' class='xr-section-summary' >Data variables: <span>(22)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-0eba6bac-fa7d-46fd-b604-d18374cedd17' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0eba6bac-fa7d-46fd-b604-d18374cedd17' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1ffbd0f2-a220-4daa-8325-3acdbe97c7c2' class='xr-var-data-in' type='checkbox'><label for='data-1ffbd0f2-a220-4daa-8325-3acdbe97c7c2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3025,7 +3025,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-f4cbe17b-2f9f-403d-bc5a-81ba808493eb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f4cbe17b-2f9f-403d-bc5a-81ba808493eb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f98e3a28-a004-4b27-9e6b-9b36b9ec43cb' class='xr-var-data-in' type='checkbox'><label for='data-f98e3a28-a004-4b27-9e6b-9b36b9ec43cb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-fee4358f-b2cc-4caf-a847-dba6d77dfb3d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fee4358f-b2cc-4caf-a847-dba6d77dfb3d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ca0c850a-fa58-427b-87a5-5d463ed475aa' class='xr-var-data-in' type='checkbox'><label for='data-ca0c850a-fa58-427b-87a5-5d463ed475aa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3081,7 +3081,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-2494957b-f1d8-4527-8123-4e8160dbaa93' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2494957b-f1d8-4527-8123-4e8160dbaa93' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-14427a29-1a8b-4732-9fbf-538eb052f5b8' class='xr-var-data-in' type='checkbox'><label for='data-14427a29-1a8b-4732-9fbf-538eb052f5b8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-34077669-191f-47e2-819b-5f853f7cd4c7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-34077669-191f-47e2-819b-5f853f7cd4c7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9b963957-8679-4cf5-adb6-e8ed0ca23008' class='xr-var-data-in' type='checkbox'><label for='data-9b963957-8679-4cf5-adb6-e8ed0ca23008' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3137,7 +3137,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-ddde51da-c82b-4807-ac01-03b6e78c481d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ddde51da-c82b-4807-ac01-03b6e78c481d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3d4f7ce9-1ffc-413d-adef-822bc2d514ac' class='xr-var-data-in' type='checkbox'><label for='data-3d4f7ce9-1ffc-413d-adef-822bc2d514ac' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-feafb3cd-8f62-48cf-b03a-b1f6f891e851' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-feafb3cd-8f62-48cf-b03a-b1f6f891e851' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-23c5f758-aa5e-42ee-90fa-7994d8348301' class='xr-var-data-in' type='checkbox'><label for='data-23c5f758-aa5e-42ee-90fa-7994d8348301' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
 the first allele, 2 for the second allele), -1 to indicate a
 missing value, or -2 to indicate a non allele in mixed ploidy datasets.</dd><dt><span>mixed_ploidy :</span></dt><dd>False</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -3219,7 +3219,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-94716708-bbf4-4109-a2ea-70630130ff3e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-94716708-bbf4-4109-a2ea-70630130ff3e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ca6a51af-33e2-4c03-8319-92dcb83538f0' class='xr-var-data-in' type='checkbox'><label for='data-ca6a51af-33e2-4c03-8319-92dcb83538f0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-f987cf5e-e202-497c-ae14-2abbe2b44546' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f987cf5e-e202-497c-ae14-2abbe2b44546' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7dfe8269-13dc-4929-b9c9-d6eb23d3cba6' class='xr-var-data-in' type='checkbox'><label for='data-7dfe8269-13dc-4929-b9c9-d6eb23d3cba6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3299,7 +3299,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-f09c4c78-0b27-4acf-b76c-b7b74614d7a3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f09c4c78-0b27-4acf-b76c-b7b74614d7a3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c29c2312-a6ca-4739-be3f-7fc84a1f179f' class='xr-var-data-in' type='checkbox'><label for='data-c29c2312-a6ca-4739-be3f-7fc84a1f179f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-099d1f65-a020-45d8-a856-6b466b815dc0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-099d1f65-a020-45d8-a856-6b466b815dc0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-901d34d5-5d79-4fb6-99fc-8c7b8ee11b40' class='xr-var-data-in' type='checkbox'><label for='data-901d34d5-5d79-4fb6-99fc-8c7b8ee11b40' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
 all calls are unphased.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -3356,7 +3356,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-25be0587-245e-4eda-a91c-c94ed843623f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-25be0587-245e-4eda-a91c-c94ed843623f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ec957b76-9c38-41b2-8274-401329fe5659' class='xr-var-data-in' type='checkbox'><label for='data-ec957b76-9c38-41b2-8274-401329fe5659' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-cca0f696-f83d-4e2e-9d67-a6090c661533' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cca0f696-f83d-4e2e-9d67-a6090c661533' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-15c066a0-87b8-45c1-8d99-8371079a5a20' class='xr-var-data-in' type='checkbox'><label for='data-15c066a0-87b8-45c1-8d99-8371079a5a20' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3411,7 +3411,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-40d66e4e-27fc-45bf-8ade-3d67da391615' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-40d66e4e-27fc-45bf-8ade-3d67da391615' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d55e6bd9-37e3-4fce-bb93-4b1fc0420aa5' class='xr-var-data-in' type='checkbox'><label for='data-d55e6bd9-37e3-4fce-bb93-4b1fc0420aa5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-eba46d40-d2c3-4e5c-bff0-d1c20e9fed4a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-eba46d40-d2c3-4e5c-bff0-d1c20e9fed4a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b8323522-ef65-4b34-ae0b-188c05433d86' class='xr-var-data-in' type='checkbox'><label for='data-b8323522-ef65-4b34-ae0b-188c05433d86' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3466,7 +3466,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-c1253083-1ae9-4b67-8e29-a32305053b0d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c1253083-1ae9-4b67-8e29-a32305053b0d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f60a6a13-39f9-4f2f-b427-0dc0502a21a1' class='xr-var-data-in' type='checkbox'><label for='data-f60a6a13-39f9-4f2f-b427-0dc0502a21a1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-771469c6-d855-4ab4-a595-0c2016ffd003' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-771469c6-d855-4ab4-a595-0c2016ffd003' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-227265d0-a1a3-40b6-8d45-b52747c73542' class='xr-var-data-in' type='checkbox'><label for='data-227265d0-a1a3-40b6-8d45-b52747c73542' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3521,7 +3521,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-c3a1dcef-3158-4530-8ba4-711c112b61bb' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c3a1dcef-3158-4530-8ba4-711c112b61bb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3e2fd7e5-2a44-4a6f-98bb-bf4aa4a93d61' class='xr-var-data-in' type='checkbox'><label for='data-3e2fd7e5-2a44-4a6f-98bb-bf4aa4a93d61' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-31465f03-4233-4692-b95c-0d88f32a2921' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-31465f03-4233-4692-b95c-0d88f32a2921' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dec834f5-cf7a-402e-b593-807b57ffc1cd' class='xr-var-data-in' type='checkbox'><label for='data-dec834f5-cf7a-402e-b593-807b57ffc1cd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3577,7 +3577,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-db97909c-7e9d-46cf-9e51-fe5f29758f0d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-db97909c-7e9d-46cf-9e51-fe5f29758f0d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a15282d5-f97f-438c-90cd-87f6b9c30c88' class='xr-var-data-in' type='checkbox'><label for='data-a15282d5-f97f-438c-90cd-87f6b9c30c88' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-63385a8a-5406-4183-91c3-e31699c119e2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-63385a8a-5406-4183-91c3-e31699c119e2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7d988b03-2924-44ad-b498-479064723dec' class='xr-var-data-in' type='checkbox'><label for='data-7d988b03-2924-44ad-b498-479064723dec' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -3635,7 +3635,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-2509ea9e-cdca-46bc-a7da-58386610731a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2509ea9e-cdca-46bc-a7da-58386610731a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6b907634-82c4-45f1-8ae8-461cad45f360' class='xr-var-data-in' type='checkbox'><label for='data-6b907634-82c4-45f1-8ae8-461cad45f360' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-ab34b761-6609-4c14-bd18-2990cadd3ab8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ab34b761-6609-4c14-bd18-2990cadd3ab8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6a054736-4499-494f-83aa-38b929e38fd7' class='xr-var-data-in' type='checkbox'><label for='data-6a054736-4499-494f-83aa-38b929e38fd7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3691,7 +3691,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-6475cca4-c086-4731-8775-d5a234472bb9' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6475cca4-c086-4731-8775-d5a234472bb9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b6f37109-fb98-4c54-815d-f943d6c14145' class='xr-var-data-in' type='checkbox'><label for='data-b6f37109-fb98-4c54-815d-f943d6c14145' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-44d3c036-9743-485d-83e6-a0df52a8b7ea' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-44d3c036-9743-485d-83e6-a0df52a8b7ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5f6137b8-f424-4d50-8425-ace1849ab5db' class='xr-var-data-in' type='checkbox'><label for='data-5f6137b8-f424-4d50-8425-ace1849ab5db' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3747,7 +3747,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-e1a40f59-a111-48c0-8f0d-843378bcbcf7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e1a40f59-a111-48c0-8f0d-843378bcbcf7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-70f29e17-7d52-4ca9-82ce-5db11a2aa7ea' class='xr-var-data-in' type='checkbox'><label for='data-70f29e17-7d52-4ca9-82ce-5db11a2aa7ea' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-fcadfe4b-bfb4-4b5f-a2df-69b0f39a8a64' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fcadfe4b-bfb4-4b5f-a2df-69b0f39a8a64' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b3015034-2d9a-4211-a034-1021f69f61be' class='xr-var-data-in' type='checkbox'><label for='data-b3015034-2d9a-4211-a034-1021f69f61be' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3803,7 +3803,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-fccca370-c6f7-49e4-b415-28da97dc50e3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-fccca370-c6f7-49e4-b415-28da97dc50e3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0e9cb2ff-915c-4db6-a8bc-38e1df06ed72' class='xr-var-data-in' type='checkbox'><label for='data-0e9cb2ff-915c-4db6-a8bc-38e1df06ed72' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-942ccd06-41aa-4538-8ff9-fc5992359b01' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-942ccd06-41aa-4538-8ff9-fc5992359b01' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-14e52292-6c35-410a-bbce-baabf8ea5b3a' class='xr-var-data-in' type='checkbox'><label for='data-14e52292-6c35-410a-bbce-baabf8ea5b3a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3859,7 +3859,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-affb80c0-13c7-42d3-b41f-adb39c6c0fca' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-affb80c0-13c7-42d3-b41f-adb39c6c0fca' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-647a292e-41db-439c-9553-f7fae08ce840' class='xr-var-data-in' type='checkbox'><label for='data-647a292e-41db-439c-9553-f7fae08ce840' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-8ebd6486-1cae-4bf6-a65f-21b29f743a93' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8ebd6486-1cae-4bf6-a65f-21b29f743a93' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5f562c99-509d-4ee1-9072-92931e8ce7c2' class='xr-var-data-in' type='checkbox'><label for='data-5f562c99-509d-4ee1-9072-92931e8ce7c2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3915,7 +3915,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-68484e7a-869c-4b5f-b064-a986d9906bb6' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-68484e7a-869c-4b5f-b064-a986d9906bb6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-76b1b22a-ef4d-420d-b3f6-961cf24d0037' class='xr-var-data-in' type='checkbox'><label for='data-76b1b22a-ef4d-420d-b3f6-961cf24d0037' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-3c569b13-c3a7-4f9c-bc3f-a4e42495ee8a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3c569b13-c3a7-4f9c-bc3f-a4e42495ee8a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-576a37e7-99e2-4fe0-bb7b-b4025d8bb0a5' class='xr-var-data-in' type='checkbox'><label for='data-576a37e7-99e2-4fe0-bb7b-b4025d8bb0a5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -3971,7 +3971,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-75564724-d9d2-4e25-bd0f-8e6c1dc971a0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-75564724-d9d2-4e25-bd0f-8e6c1dc971a0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-57fdd9c1-e5b7-499d-9cea-6e4e433278f9' class='xr-var-data-in' type='checkbox'><label for='data-57fdd9c1-e5b7-499d-9cea-6e4e433278f9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-380cd4c7-c2cf-40c1-be21-e467e4fabd54' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-380cd4c7-c2cf-40c1-be21-e467e4fabd54' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0a7fd74c-fd4f-4247-b2b4-1736074742dd' class='xr-var-data-in' type='checkbox'><label for='data-0a7fd74c-fd4f-4247-b2b4-1736074742dd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
        &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;,
@@ -4002,7 +4002,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-bc960d0b-5366-487b-9bd3-0bf77be2f79c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bc960d0b-5366-487b-9bd3-0bf77be2f79c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b4cdebbb-43bb-4205-8497-ccdc69f7a833' class='xr-var-data-in' type='checkbox'><label for='data-b4cdebbb-43bb-4205-8497-ccdc69f7a833' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-33094434-8e9b-483e-adbe-2ce097f7c2cd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-33094434-8e9b-483e-adbe-2ce097f7c2cd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0472f7ca-7616-448b-a6b4-d5bbb61e8666' class='xr-var-data-in' type='checkbox'><label for='data-0472f7ca-7616-448b-a6b4-d5bbb61e8666' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;,
@@ -4033,7 +4033,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-e1afa021-5b86-4466-8f6d-5f12d06246a9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e1afa021-5b86-4466-8f6d-5f12d06246a9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6268dc0d-0053-4094-a578-8a01498e192e' class='xr-var-data-in' type='checkbox'><label for='data-6268dc0d-0053-4094-a578-8a01498e192e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-d017b673-8330-46a7-8f56-d89e5715fe39' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d017b673-8330-46a7-8f56-d89e5715fe39' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b722dfb7-0ae4-4a99-9b9b-b84d75bcabe5' class='xr-var-data-in' type='checkbox'><label for='data-b722dfb7-0ae4-4a99-9b9b-b84d75bcabe5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
         True, False, False,  True,  True, False, False, False, False,
         True, False, False,  True, False,  True, False, False, False,
         True,  True,  True, False,  True,  True,  True, False,  True,
@@ -4064,7 +4064,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        False,  True, False, False,  True,  True, False, False, False,
         True, False,  True,  True,  True, False,  True,  True, False,
         True, False, False,  True,  True,  True,  True,  True, False,
-       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-d25cb76f-d36a-4c80-9e5c-b65043ac23a6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d25cb76f-d36a-4c80-9e5c-b65043ac23a6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-42474fe6-0496-4cfc-a2a2-15489d89ad76' class='xr-var-data-in' type='checkbox'><label for='data-42474fe6-0496-4cfc-a2a2-15489d89ad76' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
+       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-2944705b-f962-4a61-b9dd-a782d72d1101' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2944705b-f962-4a61-b9dd-a782d72d1101' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-57e23bd4-b379-44ca-b48f-e6f0d4581692' class='xr-var-data-in' type='checkbox'><label for='data-57e23bd4-b379-44ca-b48f-e6f0d4581692' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
        False,  True, False,  True,  True,  True, False, False, False,
        False,  True,  True,  True,  True,  True,  True, False,  True,
         True,  True, False,  True,  True, False,  True, False, False,
@@ -4095,7 +4095,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        False, False,  True, False, False,  True,  True, False,  True,
         True, False, False, False, False,  True,  True,  True,  True,
         True,  True,  True, False, False,  True, False, False,  True,
-        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-5bba0cd5-b840-430e-8b90-63265f990f68' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5bba0cd5-b840-430e-8b90-63265f990f68' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ac936279-0f92-435e-85f1-304ca38c654d' class='xr-var-data-in' type='checkbox'><label for='data-ac936279-0f92-435e-85f1-304ca38c654d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
+        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-a864ff97-0056-4dc9-af06-934418b84e74' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a864ff97-0056-4dc9-af06-934418b84e74' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-33f20a4e-842f-405d-8186-4f70c76f33c9' class='xr-var-data-in' type='checkbox'><label for='data-33f20a4e-842f-405d-8186-4f70c76f33c9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
        7, 5, 1, 5, 5, 5, 4, 4, 5, 5, 5, 6, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5,
        5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5, 5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4,
        6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5, 4, 4, 5, 8, 3, 4, 4, 4, 7, 5, 4,
@@ -4107,7 +4107,7 @@ <h2>Adding column fields<a class="headerlink" href="#adding-column-fields" title
        4, 5, 3, 5, 6, 5, 4, 3, 8, 2, 4, 4, 6, 8, 4, 3, 4, 3, 2, 5, 6, 6,
        4, 3, 5, 7, 4, 2, 5, 5, 6, 3, 2, 4, 4, 6, 5, 6, 5, 7, 2, 4, 2, 1,
        5, 3, 5, 3, 5, 2, 4, 9, 6, 4, 3, 4, 4, 6, 6, 7, 6, 6, 3, 4, 3, 6,
-       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-468977a0-b5fb-4a28-9ad7-645ad2c3167d' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-468977a0-b5fb-4a28-9ad7-645ad2c3167d' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-58010dba-fa28-4850-8e8f-6050b469ee9a' class='xr-section-summary-in' type='checkbox'  ><label for='section-58010dba-fa28-4850-8e8f-6050b469ee9a' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-c293d560-de5d-4166-9372-1e8aacb74680' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c293d560-de5d-4166-9372-1e8aacb74680' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-d62e49a1-4548-46f4-8e46-0abf7b07265b' class='xr-section-summary-in' type='checkbox'  ><label for='section-d62e49a1-4548-46f4-8e46-0abf7b07265b' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -4762,7 +4762,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
     isFemale              (samples) bool 284B False True False ... False True
     PurpleHair            (samples) bool 284B False False False ... True True
     CaffeineConsumption   (samples) int64 2kB 4 4 4 3 6 2 4 2 ... 6 4 6 4 6 5 5
-Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-2ba38133-200f-4f5f-a3a1-b9794f4acc9f' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2ba38133-200f-4f5f-a3a1-b9794f4acc9f' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-adb891c9-2946-4150-89ee-77415c4103ea' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-adb891c9-2946-4150-89ee-77415c4103ea' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-c3d55047-c374-45b7-b1c6-c2e8687da2a9' class='xr-section-summary-in' type='checkbox'  checked><label for='section-c3d55047-c374-45b7-b1c6-c2e8687da2a9' class='xr-section-summary' >Data variables: <span>(22)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-4f015d8a-5a63-4fbc-b3d6-ec0495728404' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4f015d8a-5a63-4fbc-b3d6-ec0495728404' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4f8057d0-fd29-4a2d-97da-8f8edea8ac7b' class='xr-var-data-in' type='checkbox'><label for='data-4f8057d0-fd29-4a2d-97da-8f8edea8ac7b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-c5436fe9-b656-4067-91b8-0680efb766f7' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c5436fe9-b656-4067-91b8-0680efb766f7' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-09f38f74-d8d1-48cc-ae99-5a3f68d092d4' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-09f38f74-d8d1-48cc-ae99-5a3f68d092d4' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-fe4ed524-f3b2-4748-9c2a-8ccfdd499ff4' class='xr-section-summary-in' type='checkbox'  checked><label for='section-fe4ed524-f3b2-4748-9c2a-8ccfdd499ff4' class='xr-section-summary' >Data variables: <span>(22)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-984ea892-fa41-443b-9a4a-6fff0b981335' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-984ea892-fa41-443b-9a4a-6fff0b981335' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3dd4713e-ca80-4b9d-be90-cdc34dd96b0f' class='xr-var-data-in' type='checkbox'><label for='data-3dd4713e-ca80-4b9d-be90-cdc34dd96b0f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -4842,7 +4842,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-8bc62ce0-fbce-4175-8bc8-bc7bf2b4a41a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8bc62ce0-fbce-4175-8bc8-bc7bf2b4a41a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3b0d1705-55c4-47bb-aa78-38a74679106e' class='xr-var-data-in' type='checkbox'><label for='data-3b0d1705-55c4-47bb-aa78-38a74679106e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-a5ecbf85-1f0f-4d73-bfec-45ef7d2d1780' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a5ecbf85-1f0f-4d73-bfec-45ef7d2d1780' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d22629e1-0a25-4783-8fc7-1c18a3058a83' class='xr-var-data-in' type='checkbox'><label for='data-d22629e1-0a25-4783-8fc7-1c18a3058a83' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -4898,7 +4898,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-0a95713b-1145-48b1-8da7-d34148db6fc4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0a95713b-1145-48b1-8da7-d34148db6fc4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d8e8eef-4418-4e81-83c3-ec1d9980015f' class='xr-var-data-in' type='checkbox'><label for='data-9d8e8eef-4418-4e81-83c3-ec1d9980015f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-c5dd0f88-420b-4919-bc84-e85f2a6da37f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c5dd0f88-420b-4919-bc84-e85f2a6da37f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e13a479f-da6d-47fd-9a37-91f6b964e093' class='xr-var-data-in' type='checkbox'><label for='data-e13a479f-da6d-47fd-9a37-91f6b964e093' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -4954,7 +4954,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-18b8af1c-d690-4eeb-b9f6-7e5aef6ca228' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-18b8af1c-d690-4eeb-b9f6-7e5aef6ca228' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-62c0b4a7-19e9-48eb-a23d-014483a6da06' class='xr-var-data-in' type='checkbox'><label for='data-62c0b4a7-19e9-48eb-a23d-014483a6da06' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-a88fd1ef-e94a-41c1-84db-9ab42a7317dd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a88fd1ef-e94a-41c1-84db-9ab42a7317dd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-be533cd2-320e-4862-8515-1ea97d5a7816' class='xr-var-data-in' type='checkbox'><label for='data-be533cd2-320e-4862-8515-1ea97d5a7816' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
 the first allele, 2 for the second allele), -1 to indicate a
 missing value, or -2 to indicate a non allele in mixed ploidy datasets.</dd><dt><span>mixed_ploidy :</span></dt><dd>False</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -5036,7 +5036,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-3b5c85f3-55a7-44e6-b6ef-1da257ab4ed3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3b5c85f3-55a7-44e6-b6ef-1da257ab4ed3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c0467318-e55e-4c5a-8c1f-3e78b711afa0' class='xr-var-data-in' type='checkbox'><label for='data-c0467318-e55e-4c5a-8c1f-3e78b711afa0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-a4eeb88b-94bd-467e-8f1f-c4db10191cee' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a4eeb88b-94bd-467e-8f1f-c4db10191cee' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6067c0f7-9236-44f3-9cc6-6c23bfd97b31' class='xr-var-data-in' type='checkbox'><label for='data-6067c0f7-9236-44f3-9cc6-6c23bfd97b31' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5116,7 +5116,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-aca06827-46c1-41da-81cd-6b06f2408da1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-aca06827-46c1-41da-81cd-6b06f2408da1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-97cde35e-94f5-4842-a1ef-eb9d7d7001e1' class='xr-var-data-in' type='checkbox'><label for='data-97cde35e-94f5-4842-a1ef-eb9d7d7001e1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-98bcd3ec-9f2c-48f1-8040-5844e0af9cf4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-98bcd3ec-9f2c-48f1-8040-5844e0af9cf4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-eff07760-c3b4-4167-9841-92e7635c7d50' class='xr-var-data-in' type='checkbox'><label for='data-eff07760-c3b4-4167-9841-92e7635c7d50' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
 all calls are unphased.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -5173,7 +5173,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-a1681782-fc07-4b62-8787-5eedf3c31e2b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a1681782-fc07-4b62-8787-5eedf3c31e2b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3d3c4448-b683-43eb-8cfe-281a6457361f' class='xr-var-data-in' type='checkbox'><label for='data-3d3c4448-b683-43eb-8cfe-281a6457361f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-1e5cdeb7-8100-44e5-b8bf-f9e625cdfbe7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1e5cdeb7-8100-44e5-b8bf-f9e625cdfbe7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-233dafbf-3e19-4996-ae49-caca45a057e4' class='xr-var-data-in' type='checkbox'><label for='data-233dafbf-3e19-4996-ae49-caca45a057e4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5228,7 +5228,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-2e188d5c-49b4-482b-9986-ee32bae51dbc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2e188d5c-49b4-482b-9986-ee32bae51dbc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-728325a8-bd86-4756-9f2d-fe40f9746f96' class='xr-var-data-in' type='checkbox'><label for='data-728325a8-bd86-4756-9f2d-fe40f9746f96' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-4be0e944-74e6-4f25-b9e6-6d5cf6072fe5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4be0e944-74e6-4f25-b9e6-6d5cf6072fe5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c055101b-672f-4fd0-8099-492cafa47650' class='xr-var-data-in' type='checkbox'><label for='data-c055101b-672f-4fd0-8099-492cafa47650' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5283,7 +5283,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-a850bcad-c7b6-4f90-9097-8230899aac2f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a850bcad-c7b6-4f90-9097-8230899aac2f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6fab3919-8a0e-402b-a944-d276981120d4' class='xr-var-data-in' type='checkbox'><label for='data-6fab3919-8a0e-402b-a944-d276981120d4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-51a2e3fb-3506-4b46-b75b-27ddfa6a027f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-51a2e3fb-3506-4b46-b75b-27ddfa6a027f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a433e3ca-d8a9-4d27-88a1-ff64bff5f0f3' class='xr-var-data-in' type='checkbox'><label for='data-a433e3ca-d8a9-4d27-88a1-ff64bff5f0f3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5338,7 +5338,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-f7a97756-392a-4d60-b60e-0b94f9cff400' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f7a97756-392a-4d60-b60e-0b94f9cff400' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-10239462-69dc-48c9-b27f-61389a940c61' class='xr-var-data-in' type='checkbox'><label for='data-10239462-69dc-48c9-b27f-61389a940c61' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-4a8999cd-2cca-4f9b-873a-cc578d8bee56' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4a8999cd-2cca-4f9b-873a-cc578d8bee56' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-445c7ea1-1ac1-4181-93ef-db0a7edb8577' class='xr-var-data-in' type='checkbox'><label for='data-445c7ea1-1ac1-4181-93ef-db0a7edb8577' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5394,7 +5394,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ba734e67-b5aa-46c7-957a-c0dc9b0fa9a1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ba734e67-b5aa-46c7-957a-c0dc9b0fa9a1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-98bd1647-2862-44e8-ae90-ebb6e3ffad85' class='xr-var-data-in' type='checkbox'><label for='data-98bd1647-2862-44e8-ae90-ebb6e3ffad85' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ffbd8787-f9ac-402d-b2c9-8688883efdd4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ffbd8787-f9ac-402d-b2c9-8688883efdd4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b5e6c28f-2aca-4a42-b943-92d85d61c432' class='xr-var-data-in' type='checkbox'><label for='data-b5e6c28f-2aca-4a42-b943-92d85d61c432' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -5452,7 +5452,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-9fbf9c6f-edd6-4f7e-b5fa-e5d0541b7d84' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9fbf9c6f-edd6-4f7e-b5fa-e5d0541b7d84' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1cbf5abe-687d-46aa-976a-2c8010634db9' class='xr-var-data-in' type='checkbox'><label for='data-1cbf5abe-687d-46aa-976a-2c8010634db9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-356ffcf2-9ed1-4769-9227-69a659e4736d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-356ffcf2-9ed1-4769-9227-69a659e4736d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bae252ad-58fb-4a7b-b580-3eb06c4e21be' class='xr-var-data-in' type='checkbox'><label for='data-bae252ad-58fb-4a7b-b580-3eb06c4e21be' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5508,7 +5508,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-76d54ac6-3064-4356-9916-768185a95f56' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-76d54ac6-3064-4356-9916-768185a95f56' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ddabe6f8-53c5-49be-97e7-5592549dd001' class='xr-var-data-in' type='checkbox'><label for='data-ddabe6f8-53c5-49be-97e7-5592549dd001' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-50c95342-caf6-404c-b26e-e8ee3df38cb8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-50c95342-caf6-404c-b26e-e8ee3df38cb8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-83ca3278-e622-4e27-b54e-3940d5c35ff6' class='xr-var-data-in' type='checkbox'><label for='data-83ca3278-e622-4e27-b54e-3940d5c35ff6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5564,7 +5564,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-a91182e1-2924-4140-82f8-cfa9b8284256' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a91182e1-2924-4140-82f8-cfa9b8284256' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fbf5da41-b618-4908-b6c3-a0df0bad5631' class='xr-var-data-in' type='checkbox'><label for='data-fbf5da41-b618-4908-b6c3-a0df0bad5631' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-105ac2b3-d651-462a-ab69-74cf353f95df' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-105ac2b3-d651-462a-ab69-74cf353f95df' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-acf0c21a-a11e-4693-a8e6-48ad0e544132' class='xr-var-data-in' type='checkbox'><label for='data-acf0c21a-a11e-4693-a8e6-48ad0e544132' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5620,7 +5620,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-298c5a5d-0301-43f8-9b8a-272564d629b2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-298c5a5d-0301-43f8-9b8a-272564d629b2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-395ec62b-93d0-444d-87d6-2ff18d4cf1be' class='xr-var-data-in' type='checkbox'><label for='data-395ec62b-93d0-444d-87d6-2ff18d4cf1be' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-4978e3c2-45e5-4021-ad8f-592b613c02fe' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4978e3c2-45e5-4021-ad8f-592b613c02fe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8253c42e-d8ea-479e-9d1b-49ede164e7d7' class='xr-var-data-in' type='checkbox'><label for='data-8253c42e-d8ea-479e-9d1b-49ede164e7d7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5676,7 +5676,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-12a83d8d-db6b-4b6c-8095-0b974da2029b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-12a83d8d-db6b-4b6c-8095-0b974da2029b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e663d36b-9434-4d58-9296-4993c04a7d9d' class='xr-var-data-in' type='checkbox'><label for='data-e663d36b-9434-4d58-9296-4993c04a7d9d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-0ccefac2-7782-4cfa-8e8a-9ed4f532d000' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0ccefac2-7782-4cfa-8e8a-9ed4f532d000' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4a8664e3-baee-4de0-bf2c-99ddfb8b7d77' class='xr-var-data-in' type='checkbox'><label for='data-4a8664e3-baee-4de0-bf2c-99ddfb8b7d77' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5732,7 +5732,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d4303c5b-0bd6-4c36-a207-83b49ecbcc21' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d4303c5b-0bd6-4c36-a207-83b49ecbcc21' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-97b4dc94-fc7f-4cdc-8b4f-ca91df020122' class='xr-var-data-in' type='checkbox'><label for='data-97b4dc94-fc7f-4cdc-8b4f-ca91df020122' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d75fed69-7761-4987-aada-59932baf2ea7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d75fed69-7761-4987-aada-59932baf2ea7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fc9c473b-e03e-4a79-b671-3cd128605b62' class='xr-var-data-in' type='checkbox'><label for='data-fc9c473b-e03e-4a79-b671-3cd128605b62' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -5788,7 +5788,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-a31e32f1-001d-44c8-807b-9a363faffb00' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a31e32f1-001d-44c8-807b-9a363faffb00' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2ccabb08-8be9-4e05-8792-d9d55b2a1686' class='xr-var-data-in' type='checkbox'><label for='data-2ccabb08-8be9-4e05-8792-d9d55b2a1686' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-702c1da5-5da4-43db-8257-c35b429c9887' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-702c1da5-5da4-43db-8257-c35b429c9887' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-68fe92d6-1e61-4d2a-a5ef-8cc49ed309ad' class='xr-var-data-in' type='checkbox'><label for='data-68fe92d6-1e61-4d2a-a5ef-8cc49ed309ad' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
        &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;,
@@ -5819,7 +5819,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-d6f4b88f-c1df-4e65-bafa-37bc401c9971' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d6f4b88f-c1df-4e65-bafa-37bc401c9971' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e129334f-4387-44ff-b6eb-1c1a7d24abdf' class='xr-var-data-in' type='checkbox'><label for='data-e129334f-4387-44ff-b6eb-1c1a7d24abdf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-6f17d9d2-dea2-4dc8-af20-677fad2afdd5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6f17d9d2-dea2-4dc8-af20-677fad2afdd5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6de5c9ca-558f-4350-987d-e1a770f9b2b1' class='xr-var-data-in' type='checkbox'><label for='data-6de5c9ca-558f-4350-987d-e1a770f9b2b1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;,
@@ -5850,7 +5850,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-c39f9eb2-3c53-42d9-91fa-e57fe0b1f327' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c39f9eb2-3c53-42d9-91fa-e57fe0b1f327' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f36ad511-a87f-465f-a1cc-f2e7b9004c73' class='xr-var-data-in' type='checkbox'><label for='data-f36ad511-a87f-465f-a1cc-f2e7b9004c73' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-2bfacba1-7c78-45ff-a7b2-74ce51c5f1cd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2bfacba1-7c78-45ff-a7b2-74ce51c5f1cd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4ec7b14a-5a93-4f94-9eb6-bbf713bb6ccf' class='xr-var-data-in' type='checkbox'><label for='data-4ec7b14a-5a93-4f94-9eb6-bbf713bb6ccf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
         True, False, False,  True,  True, False, False, False, False,
         True, False, False,  True, False,  True, False, False, False,
         True,  True,  True, False,  True,  True,  True, False,  True,
@@ -5881,7 +5881,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False,  True, False, False,  True,  True, False, False, False,
         True, False,  True,  True,  True, False,  True,  True, False,
         True, False, False,  True,  True,  True,  True,  True, False,
-       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-945f98e7-9149-42da-9d9d-d0fa781808ee' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-945f98e7-9149-42da-9d9d-d0fa781808ee' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3d0c8a43-f832-432a-a91c-24e97929f8b0' class='xr-var-data-in' type='checkbox'><label for='data-3d0c8a43-f832-432a-a91c-24e97929f8b0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
+       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-496009ff-4db1-48ce-a4a4-2a4c94f63a56' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-496009ff-4db1-48ce-a4a4-2a4c94f63a56' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6714250a-eedc-4ce1-b63d-5662d947be72' class='xr-var-data-in' type='checkbox'><label for='data-6714250a-eedc-4ce1-b63d-5662d947be72' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
        False,  True, False,  True,  True,  True, False, False, False,
        False,  True,  True,  True,  True,  True,  True, False,  True,
         True,  True, False,  True,  True, False,  True, False, False,
@@ -5912,7 +5912,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False, False,  True, False, False,  True,  True, False,  True,
         True, False, False, False, False,  True,  True,  True,  True,
         True,  True,  True, False, False,  True, False, False,  True,
-        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-75b19b5e-b503-47eb-9fba-f994604a7e8d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-75b19b5e-b503-47eb-9fba-f994604a7e8d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fbf1d354-23dd-4fd4-962f-430e695a9599' class='xr-var-data-in' type='checkbox'><label for='data-fbf1d354-23dd-4fd4-962f-430e695a9599' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
+        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-da08fd67-601d-4f43-b680-d68400f385eb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-da08fd67-601d-4f43-b680-d68400f385eb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5f181ffd-346b-44ed-a81e-ead8f29fb6a2' class='xr-var-data-in' type='checkbox'><label for='data-5f181ffd-346b-44ed-a81e-ead8f29fb6a2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
        7, 5, 1, 5, 5, 5, 4, 4, 5, 5, 5, 6, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5,
        5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5, 5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4,
        6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5, 4, 4, 5, 8, 3, 4, 4, 4, 7, 5, 4,
@@ -5924,7 +5924,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        4, 5, 3, 5, 6, 5, 4, 3, 8, 2, 4, 4, 6, 8, 4, 3, 4, 3, 2, 5, 6, 6,
        4, 3, 5, 7, 4, 2, 5, 5, 6, 3, 2, 4, 4, 6, 5, 6, 5, 7, 2, 4, 2, 1,
        5, 3, 5, 3, 5, 2, 4, 9, 6, 4, 3, 4, 4, 6, 6, 7, 6, 6, 3, 4, 3, 6,
-       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-552c7cb2-b462-403b-852e-28992ada4bd2' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-552c7cb2-b462-403b-852e-28992ada4bd2' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-3eb0627c-7613-4814-84c6-f94b6e35fae1' class='xr-section-summary-in' type='checkbox'  ><label for='section-3eb0627c-7613-4814-84c6-f94b6e35fae1' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-a79e49b7-40bf-420f-9a5a-d2f92d38764c' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-a79e49b7-40bf-420f-9a5a-d2f92d38764c' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-efa2a64a-72ca-4e43-8b3a-6eb1e64f2a4b' class='xr-section-summary-in' type='checkbox'  ><label for='section-efa2a64a-72ca-4e43-8b3a-6eb1e64f2a4b' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -6429,7 +6429,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
     isFemale              (samples) bool 284B False True False ... False True
     PurpleHair            (samples) bool 284B False False False ... True True
     CaffeineConsumption   (samples) int64 2kB 4 4 4 3 6 2 4 2 ... 6 4 6 4 6 5 5
-Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-88d94449-d975-4ddf-b2f7-a41f481feb01' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-88d94449-d975-4ddf-b2f7-a41f481feb01' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-ce677500-41ba-41d5-8c62-3b556d3edcd7' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-ce677500-41ba-41d5-8c62-3b556d3edcd7' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-981df60e-1ba9-48d9-823b-ad7520d4e408' class='xr-section-summary-in' type='checkbox'  checked><label for='section-981df60e-1ba9-48d9-823b-ad7520d4e408' class='xr-section-summary' >Data variables: <span>(28)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-d4487f88-81e6-499e-b641-d26202e85d9e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d4487f88-81e6-499e-b641-d26202e85d9e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c5154bbc-5413-42fc-abe8-5e6b82f1338b' class='xr-var-data-in' type='checkbox'><label for='data-c5154bbc-5413-42fc-abe8-5e6b82f1338b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-c9eb9dc5-c53b-4e4d-b28a-b044a026cab0' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-c9eb9dc5-c53b-4e4d-b28a-b044a026cab0' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 284</li><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-34c8f662-5e0f-4154-926b-e57b7bda4228' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-34c8f662-5e0f-4154-926b-e57b7bda4228' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-3f3eaa1f-94c2-49a4-be50-ddd4afe1f9a1' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3f3eaa1f-94c2-49a4-be50-ddd4afe1f9a1' class='xr-section-summary' >Data variables: <span>(28)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-4f879649-f289-4a68-b7bf-8cd2bef6a4cf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4f879649-f289-4a68-b7bf-8cd2bef6a4cf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a4eeb7b2-3e16-4d2f-885a-96dcc16a0005' class='xr-var-data-in' type='checkbox'><label for='data-a4eeb7b2-3e16-4d2f-885a-96dcc16a0005' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6484,7 +6484,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-2484b0ea-d1cd-4f26-8b83-b778f7754933' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2484b0ea-d1cd-4f26-8b83-b778f7754933' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-740f999b-b6a7-4a83-ad6d-996db325c4b5' class='xr-var-data-in' type='checkbox'><label for='data-740f999b-b6a7-4a83-ad6d-996db325c4b5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-e30ed432-b5c9-4b4b-90d8-a43370830532' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e30ed432-b5c9-4b4b-90d8-a43370830532' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c75d11f9-4015-43c8-88bd-e945db2034c2' class='xr-var-data-in' type='checkbox'><label for='data-c75d11f9-4015-43c8-88bd-e945db2034c2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6539,7 +6539,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-47c3701c-2835-4b37-b597-aa4dd6ea536b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-47c3701c-2835-4b37-b597-aa4dd6ea536b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c28ef97b-60b3-423c-bfc5-6cad9e3cf539' class='xr-var-data-in' type='checkbox'><label for='data-c28ef97b-60b3-423c-bfc5-6cad9e3cf539' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-24300542-a29f-4ee6-b0a6-e2d9c8e8bfbd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-24300542-a29f-4ee6-b0a6-e2d9c8e8bfbd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8b20ee33-7378-4f83-93f0-27cf93c0e9c6' class='xr-var-data-in' type='checkbox'><label for='data-8b20ee33-7378-4f83-93f0-27cf93c0e9c6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6594,7 +6594,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-1de11666-60d5-45ed-8a1c-9341fada4c42' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1de11666-60d5-45ed-8a1c-9341fada4c42' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-27b96cb2-6727-4dbc-8120-9b8d957d17d6' class='xr-var-data-in' type='checkbox'><label for='data-27b96cb2-6727-4dbc-8120-9b8d957d17d6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-8cb73628-d78b-4a9e-82b1-7297bb3eecfc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8cb73628-d78b-4a9e-82b1-7297bb3eecfc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2e693c45-e788-42ef-a453-fcd4fc39e785' class='xr-var-data-in' type='checkbox'><label for='data-2e693c45-e788-42ef-a453-fcd4fc39e785' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6649,7 +6649,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-40f52164-51b2-4d20-ab8c-89838ec63fb6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-40f52164-51b2-4d20-ab8c-89838ec63fb6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8f704ce2-d740-493e-a375-da4934aa17da' class='xr-var-data-in' type='checkbox'><label for='data-8f704ce2-d740-493e-a375-da4934aa17da' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-00385efa-a9dc-4acf-86fa-29ef58985e8e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-00385efa-a9dc-4acf-86fa-29ef58985e8e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bb13ee34-c79c-4832-a503-31e1d34f62e0' class='xr-var-data-in' type='checkbox'><label for='data-bb13ee34-c79c-4832-a503-31e1d34f62e0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6704,7 +6704,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-628ec9db-23c0-4914-854c-52f452d40c7e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-628ec9db-23c0-4914-854c-52f452d40c7e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e2b13550-54fc-45cd-963e-82fcd6c7ea66' class='xr-var-data-in' type='checkbox'><label for='data-e2b13550-54fc-45cd-963e-82fcd6c7ea66' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(284,), meta=np.ndarray&gt;</div><input id='attrs-2c1d6b16-911e-4dea-9b75-2f261d58e289' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2c1d6b16-911e-4dea-9b75-2f261d58e289' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8791c59f-7926-4742-a1d4-7f605d5a9298' class='xr-var-data-in' type='checkbox'><label for='data-8791c59f-7926-4742-a1d4-7f605d5a9298' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6759,7 +6759,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-ecdf51d0-5f17-4326-acf3-420c1335b72d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ecdf51d0-5f17-4326-acf3-420c1335b72d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-92037a4f-353a-4152-bbeb-a5cf898a3c99' class='xr-var-data-in' type='checkbox'><label for='data-92037a4f-353a-4152-bbeb-a5cf898a3c99' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-537f3942-2e70-4be2-8943-a16ecdfdfcb9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-537f3942-2e70-4be2-8943-a16ecdfdfcb9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ef377ad4-8c6e-419d-8cfd-f524baef6e12' class='xr-var-data-in' type='checkbox'><label for='data-ef377ad4-8c6e-419d-8cfd-f524baef6e12' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6839,7 +6839,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-26b9c834-8fa6-4831-bd78-5f96355a86ae' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-26b9c834-8fa6-4831-bd78-5f96355a86ae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e99ace0a-aa88-457e-acb3-a399d5fc63c9' class='xr-var-data-in' type='checkbox'><label for='data-e99ace0a-aa88-457e-acb3-a399d5fc63c9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-a9f4114d-1364-4ed9-9e90-2920de1e3b44' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a9f4114d-1364-4ed9-9e90-2920de1e3b44' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5b9128e4-2164-4a60-9b90-d75c94d24a7f' class='xr-var-data-in' type='checkbox'><label for='data-5b9128e4-2164-4a60-9b90-d75c94d24a7f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6895,7 +6895,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-7432e17a-070b-4c25-a77a-7187e0320633' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7432e17a-070b-4c25-a77a-7187e0320633' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e9fe11ce-3196-4a45-a420-7c31337888d0' class='xr-var-data-in' type='checkbox'><label for='data-e9fe11ce-3196-4a45-a420-7c31337888d0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-51e1cd74-3a8f-432d-8d43-af7f9e6f5ece' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-51e1cd74-3a8f-432d-8d43-af7f9e6f5ece' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8bc87e59-dff8-4478-88df-fa2c49af6c0f' class='xr-var-data-in' type='checkbox'><label for='data-8bc87e59-dff8-4478-88df-fa2c49af6c0f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -6951,7 +6951,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-5eaf4a9e-1e19-40f4-b77d-fd9c0bcd319f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5eaf4a9e-1e19-40f4-b77d-fd9c0bcd319f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-309ee1cc-5117-49c6-adff-ad2047fa43f3' class='xr-var-data-in' type='checkbox'><label for='data-309ee1cc-5117-49c6-adff-ad2047fa43f3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-5d174e5b-61a2-457b-a9a2-d63a6a041cd5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5d174e5b-61a2-457b-a9a2-d63a6a041cd5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d00a0502-850a-49dd-b850-c0b0b30b6f76' class='xr-var-data-in' type='checkbox'><label for='data-d00a0502-850a-49dd-b850-c0b0b30b6f76' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
 the first allele, 2 for the second allele), -1 to indicate a
 missing value, or -2 to indicate a non allele in mixed ploidy datasets.</dd><dt><span>mixed_ploidy :</span></dt><dd>False</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -7033,7 +7033,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-f24a7388-7cf2-479b-ba52-06bd67a8ebff' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f24a7388-7cf2-479b-ba52-06bd67a8ebff' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-413e8566-fda9-4712-a386-33aca3eb945e' class='xr-var-data-in' type='checkbox'><label for='data-413e8566-fda9-4712-a386-33aca3eb945e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284, 2), meta=np.ndarray&gt;</div><input id='attrs-272df039-4696-401e-83a8-cd7a6500625d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-272df039-4696-401e-83a8-cd7a6500625d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6bb9e635-3a1e-4c5e-929e-25ae497c43fc' class='xr-var-data-in' type='checkbox'><label for='data-6bb9e635-3a1e-4c5e-929e-25ae497c43fc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7113,7 +7113,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-3c5bf19a-58fd-4b1a-a35d-16d5d3dc8362' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3c5bf19a-58fd-4b1a-a35d-16d5d3dc8362' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1d40b101-75f5-4027-85dd-b81105ef4538' class='xr-var-data-in' type='checkbox'><label for='data-1d40b101-75f5-4027-85dd-b81105ef4538' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 284), meta=np.ndarray&gt;</div><input id='attrs-d2498649-6856-4015-b852-68789ac3c5bd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d2498649-6856-4015-b852-68789ac3c5bd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d891c249-0b93-4b53-b739-e9c177eacbf3' class='xr-var-data-in' type='checkbox'><label for='data-d891c249-0b93-4b53-b739-e9c177eacbf3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
 all calls are unphased.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -7170,7 +7170,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-7b48ae3b-38e7-48be-8700-1f9a479d4346' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7b48ae3b-38e7-48be-8700-1f9a479d4346' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d34be872-4bd9-4d37-9015-aae8ab3bb2dc' class='xr-var-data-in' type='checkbox'><label for='data-d34be872-4bd9-4d37-9015-aae8ab3bb2dc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-aaa64d5b-bd9d-4f7c-8c6d-951d6b13d383' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-aaa64d5b-bd9d-4f7c-8c6d-951d6b13d383' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8cb7ee9f-ffcd-4210-a170-140694a8159f' class='xr-var-data-in' type='checkbox'><label for='data-8cb7ee9f-ffcd-4210-a170-140694a8159f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7225,7 +7225,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-2dd8a5a7-e1bf-4cdc-84cb-a2f7f24157ef' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2dd8a5a7-e1bf-4cdc-84cb-a2f7f24157ef' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf683836-db44-4df9-a477-34240878d019' class='xr-var-data-in' type='checkbox'><label for='data-bf683836-db44-4df9-a477-34240878d019' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-d4f82748-806f-430d-b097-3cc4d072bfcf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d4f82748-806f-430d-b097-3cc4d072bfcf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-73a31ea0-6ea0-416f-bd55-6b26102a71a4' class='xr-var-data-in' type='checkbox'><label for='data-73a31ea0-6ea0-416f-bd55-6b26102a71a4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7280,7 +7280,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-8239fd17-400e-4b31-ab14-155e7cf7a725' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8239fd17-400e-4b31-ab14-155e7cf7a725' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-80b16008-7f08-405e-b596-3caae98403af' class='xr-var-data-in' type='checkbox'><label for='data-80b16008-7f08-405e-b596-3caae98403af' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-ac9e8bd3-1433-4a13-9faf-e8e0cf79f955' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ac9e8bd3-1433-4a13-9faf-e8e0cf79f955' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-30f3734b-aeba-442d-a26a-c68d3a714643' class='xr-var-data-in' type='checkbox'><label for='data-30f3734b-aeba-442d-a26a-c68d3a714643' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7335,7 +7335,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-75a8c81c-ef93-4e24-ada0-f8ad264afb30' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-75a8c81c-ef93-4e24-ada0-f8ad264afb30' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b994241e-ec87-4232-ad82-f3a7405afe20' class='xr-var-data-in' type='checkbox'><label for='data-b994241e-ec87-4232-ad82-f3a7405afe20' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-6600e41d-9735-4165-be86-65aafb09ab41' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6600e41d-9735-4165-be86-65aafb09ab41' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d0413834-bb8b-42a8-a6d6-04b919b42d0c' class='xr-var-data-in' type='checkbox'><label for='data-d0413834-bb8b-42a8-a6d6-04b919b42d0c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7391,7 +7391,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-16f815fb-adef-4372-adcd-8a291ab4c5fe' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-16f815fb-adef-4372-adcd-8a291ab4c5fe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3358e566-a9de-42e8-adb4-6b501d2219e3' class='xr-var-data-in' type='checkbox'><label for='data-3358e566-a9de-42e8-adb4-6b501d2219e3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-162de6f5-056e-4cb8-81e1-97bb6202392e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-162de6f5-056e-4cb8-81e1-97bb6202392e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fa0ab502-2241-4ac2-b87c-4d473295e83f' class='xr-var-data-in' type='checkbox'><label for='data-fa0ab502-2241-4ac2-b87c-4d473295e83f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -7449,7 +7449,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-9f73a45c-eaec-43bb-aa6d-a718bb1ca81a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9f73a45c-eaec-43bb-aa6d-a718bb1ca81a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-594b9eb1-4931-43a5-842c-4ad608f85539' class='xr-var-data-in' type='checkbox'><label for='data-594b9eb1-4931-43a5-842c-4ad608f85539' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-b30760e2-1b2e-4d26-9b81-97c6d14192db' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b30760e2-1b2e-4d26-9b81-97c6d14192db' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8b931863-938b-4231-8161-f380e705075d' class='xr-var-data-in' type='checkbox'><label for='data-8b931863-938b-4231-8161-f380e705075d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7505,7 +7505,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-5e63a5d2-a371-4b24-88d6-86ead3ec6cb4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5e63a5d2-a371-4b24-88d6-86ead3ec6cb4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5de74530-3f5e-4f87-a791-a6582196a6ad' class='xr-var-data-in' type='checkbox'><label for='data-5de74530-3f5e-4f87-a791-a6582196a6ad' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-40d18722-71d4-4010-ad67-7ef75b757a42' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-40d18722-71d4-4010-ad67-7ef75b757a42' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-14361c34-02e3-4c14-a547-408ae918df7b' class='xr-var-data-in' type='checkbox'><label for='data-14361c34-02e3-4c14-a547-408ae918df7b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7561,7 +7561,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-100464f5-73a5-4582-b585-c2d293fb6a4a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-100464f5-73a5-4582-b585-c2d293fb6a4a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e0671c63-d2ce-422d-b78f-e2d95767dc96' class='xr-var-data-in' type='checkbox'><label for='data-e0671c63-d2ce-422d-b78f-e2d95767dc96' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-c59c9699-cf82-4677-8208-cde4f78983a2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c59c9699-cf82-4677-8208-cde4f78983a2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2b732137-af84-4a5e-8478-971ec1e9a3f2' class='xr-var-data-in' type='checkbox'><label for='data-2b732137-af84-4a5e-8478-971ec1e9a3f2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7617,7 +7617,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-6ae4e144-482b-4f6c-bacd-5a7fb7bb8532' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6ae4e144-482b-4f6c-bacd-5a7fb7bb8532' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fc961cae-d2da-4187-96e5-be84825a6eb5' class='xr-var-data-in' type='checkbox'><label for='data-fc961cae-d2da-4187-96e5-be84825a6eb5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-10e55eed-30ad-4545-9970-86603c0c9352' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-10e55eed-30ad-4545-9970-86603c0c9352' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2d4ff4f8-435c-473f-b07b-bd6fa0f19298' class='xr-var-data-in' type='checkbox'><label for='data-2d4ff4f8-435c-473f-b07b-bd6fa0f19298' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7673,7 +7673,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d56f44a8-0fb9-435d-9963-dbe9716ffe08' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d56f44a8-0fb9-435d-9963-dbe9716ffe08' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6a7f41de-da91-406e-ab71-be6ff982b493' class='xr-var-data-in' type='checkbox'><label for='data-6a7f41de-da91-406e-ab71-be6ff982b493' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-a05bf7a5-7e65-44f9-bb78-34376721028f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a05bf7a5-7e65-44f9-bb78-34376721028f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-01c50c26-f5a4-453a-a064-1fbeefba5867' class='xr-var-data-in' type='checkbox'><label for='data-01c50c26-f5a4-453a-a064-1fbeefba5867' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7729,7 +7729,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-0b4c96e5-5ae3-4537-8c98-487e84658646' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0b4c96e5-5ae3-4537-8c98-487e84658646' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-40215afb-c4e4-4237-8333-ac24f25e4b4f' class='xr-var-data-in' type='checkbox'><label for='data-40215afb-c4e4-4237-8333-ac24f25e4b4f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-f82fac7e-756a-40b6-914a-9b3b79ea6f76' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f82fac7e-756a-40b6-914a-9b3b79ea6f76' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-906c43bb-5644-4a2c-b1bb-8728d2c7b427' class='xr-var-data-in' type='checkbox'><label for='data-906c43bb-5644-4a2c-b1bb-8728d2c7b427' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -7785,7 +7785,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-2f3e9f1c-f8da-4547-bf4e-10602c1d6568' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2f3e9f1c-f8da-4547-bf4e-10602c1d6568' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7000c363-869b-4287-bd7d-800095c32c8a' class='xr-var-data-in' type='checkbox'><label for='data-7000c363-869b-4287-bd7d-800095c32c8a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-dcf9ea1e-ee05-4840-9182-9122dcc5e2a5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dcf9ea1e-ee05-4840-9182-9122dcc5e2a5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1eebdb55-2a67-4100-9917-9547b2e4d45a' class='xr-var-data-in' type='checkbox'><label for='data-1eebdb55-2a67-4100-9917-9547b2e4d45a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;GBR&#x27;,
        &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;,
@@ -7816,7 +7816,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-7c79ff34-27ff-4a27-b9a7-e303774fd0dc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7c79ff34-27ff-4a27-b9a7-e303774fd0dc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bc07ddb0-d184-462b-929f-76b34f038ccf' class='xr-var-data-in' type='checkbox'><label for='data-bc07ddb0-d184-462b-929f-76b34f038ccf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-71ac8644-9d5a-47a1-9a64-cd995ff4d2a1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-71ac8644-9d5a-47a1-9a64-cd995ff4d2a1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d1df316e-ccee-4cbc-be2f-bb6d305b8731' class='xr-var-data-in' type='checkbox'><label for='data-d1df316e-ccee-4cbc-be2f-bb6d305b8731' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;,
@@ -7847,7 +7847,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-8bd624bb-3037-4c28-87f0-2ef7431b14a3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8bd624bb-3037-4c28-87f0-2ef7431b14a3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4be07b8b-181f-4cc0-9ebb-345a7fdd6688' class='xr-var-data-in' type='checkbox'><label for='data-4be07b8b-181f-4cc0-9ebb-345a7fdd6688' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-60fdd9dc-3a60-4888-90e5-49259785231c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-60fdd9dc-3a60-4888-90e5-49259785231c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d0d32622-f310-4fe2-bd36-069d22592a46' class='xr-var-data-in' type='checkbox'><label for='data-d0d32622-f310-4fe2-bd36-069d22592a46' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False, False,
         True, False, False,  True,  True, False, False, False, False,
         True, False, False,  True, False,  True, False, False, False,
         True,  True,  True, False,  True,  True,  True, False,  True,
@@ -7878,7 +7878,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False,  True, False, False,  True,  True, False, False, False,
         True, False,  True,  True,  True, False,  True,  True, False,
         True, False, False,  True,  True,  True,  True,  True, False,
-       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-23825a27-532c-4e21-a435-e2766a68e9a5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-23825a27-532c-4e21-a435-e2766a68e9a5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c38ff2ee-0399-4da0-9042-10e327c12c5f' class='xr-var-data-in' type='checkbox'><label for='data-c38ff2ee-0399-4da0-9042-10e327c12c5f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
+       False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-fa071c25-a6a7-427a-a4bd-dadf4b87aae7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fa071c25-a6a7-427a-a4bd-dadf4b87aae7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-05f03274-ad78-4bf8-b261-fbfba4919341' class='xr-var-data-in' type='checkbox'><label for='data-05f03274-ad78-4bf8-b261-fbfba4919341' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True,  True, False, False,
        False,  True, False,  True,  True,  True, False, False, False,
        False,  True,  True,  True,  True,  True,  True, False,  True,
         True,  True, False,  True,  True, False,  True, False, False,
@@ -7909,7 +7909,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False, False,  True, False, False,  True,  True, False,  True,
         True, False, False, False, False,  True,  True,  True,  True,
         True,  True,  True, False, False,  True, False, False,  True,
-        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-c03d3768-1d6f-4872-8c19-73ec93dc9264' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c03d3768-1d6f-4872-8c19-73ec93dc9264' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-198d87d1-69f6-4f79-8478-a516e276a2b0' class='xr-var-data-in' type='checkbox'><label for='data-198d87d1-69f6-4f79-8478-a516e276a2b0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
+        True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 4 2 ... 5 6 4 6 4 6 5 5</div><input id='attrs-2b62480b-b386-457d-be20-39a351ba21ce' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2b62480b-b386-457d-be20-39a351ba21ce' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5a84635f-ef8f-4900-b4e0-75dbf293b216' class='xr-var-data-in' type='checkbox'><label for='data-5a84635f-ef8f-4900-b4e0-75dbf293b216' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 4, 2, 1, 2, 0, 5, 4, 5, 4, 3, 6, 5, 5, 7, 5, 5,
        7, 5, 1, 5, 5, 5, 4, 4, 5, 5, 5, 6, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5,
        5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5, 5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4,
        6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5, 4, 4, 5, 8, 3, 4, 4, 4, 7, 5, 4,
@@ -7921,7 +7921,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        4, 5, 3, 5, 6, 5, 4, 3, 8, 2, 4, 4, 6, 8, 4, 3, 4, 3, 2, 5, 6, 6,
        4, 3, 5, 7, 4, 2, 5, 5, 6, 3, 2, 4, 4, 6, 5, 6, 5, 7, 2, 4, 2, 1,
        5, 3, 5, 3, 5, 2, 4, 9, 6, 4, 3, 4, 4, 6, 6, 7, 6, 6, 3, 4, 3, 6,
-       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-48ff7244-6c03-426c-8780-639673920e73' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-48ff7244-6c03-426c-8780-639673920e73' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-fdfe1ac1-f628-4163-b5b5-0598e21a555e' class='xr-section-summary-in' type='checkbox'  ><label for='section-fdfe1ac1-f628-4163-b5b5-0598e21a555e' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+       6, 3, 4, 4, 2, 4, 6, 7, 4, 5, 4, 5, 5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-0290b982-b7a0-487a-ac8d-7e9ac541cefe' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-0290b982-b7a0-487a-ac8d-7e9ac541cefe' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-35d90a10-8cd7-4126-871e-c686bdcb9e22' class='xr-section-summary-in' type='checkbox'  ><label for='section-35d90a10-8cd7-4126-871e-c686bdcb9e22' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -8518,7 +8518,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
     PurpleHair                (samples) bool 250B False False ... True True
     CaffeineConsumption       (samples) int64 2kB 4 4 4 3 6 2 2 ... 4 6 4 6 5 5
     sample_dp_mean            (samples) float64 2kB dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;
-Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-ca9e1939-88b7-4d64-974b-da0d065430a6' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-ca9e1939-88b7-4d64-974b-da0d065430a6' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-b29d2c54-3292-4dfd-b5c5-3b3c9f0f6de0' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-b29d2c54-3292-4dfd-b5c5-3b3c9f0f6de0' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-3fb04548-11a9-40c9-92b0-2cfca06ae1aa' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3fb04548-11a9-40c9-92b0-2cfca06ae1aa' class='xr-section-summary' >Data variables: <span>(38)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-9772df06-800a-42d8-89bb-480734b21204' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9772df06-800a-42d8-89bb-480734b21204' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-47b51dea-362d-4a76-bb45-d08de76b96f9' class='xr-var-data-in' type='checkbox'><label for='data-47b51dea-362d-4a76-bb45-d08de76b96f9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-b5993107-470d-4104-abf4-c18ec1eb700a' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-b5993107-470d-4104-abf4-c18ec1eb700a' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-d8f537c1-20f7-4bb8-89f7-5af3bd885d6e' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-d8f537c1-20f7-4bb8-89f7-5af3bd885d6e' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-e88dd87e-6617-41a0-801c-c36116422362' class='xr-section-summary-in' type='checkbox'  checked><label for='section-e88dd87e-6617-41a0-801c-c36116422362' class='xr-section-summary' >Data variables: <span>(38)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-4643e8a7-5f83-44f5-b543-86ce26902f76' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4643e8a7-5f83-44f5-b543-86ce26902f76' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-47a73bdd-1451-4863-af05-3ba35309a314' class='xr-var-data-in' type='checkbox'><label for='data-47a73bdd-1451-4863-af05-3ba35309a314' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8574,7 +8574,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-03492eb9-6344-4f5b-89b5-0b24d671b712' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-03492eb9-6344-4f5b-89b5-0b24d671b712' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-374c974b-7851-4f07-b57a-076660d9c3c3' class='xr-var-data-in' type='checkbox'><label for='data-374c974b-7851-4f07-b57a-076660d9c3c3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-415d2c3a-09b8-46f9-9fb6-b582cf42e945' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-415d2c3a-09b8-46f9-9fb6-b582cf42e945' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3e944398-5ddc-4f0a-b3af-590128b188b2' class='xr-var-data-in' type='checkbox'><label for='data-3e944398-5ddc-4f0a-b3af-590128b188b2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8630,7 +8630,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-edfc241b-8148-4c4d-acc3-87c010678be7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-edfc241b-8148-4c4d-acc3-87c010678be7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dfdd4e21-2a17-4f5c-b401-b1614aaaa6f7' class='xr-var-data-in' type='checkbox'><label for='data-dfdd4e21-2a17-4f5c-b401-b1614aaaa6f7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b6b9f0e9-8f03-4f33-b714-33d9ef5b890a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b6b9f0e9-8f03-4f33-b714-33d9ef5b890a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7c677c54-296b-4bd1-b5cd-9bd4f1703638' class='xr-var-data-in' type='checkbox'><label for='data-7c677c54-296b-4bd1-b5cd-9bd4f1703638' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8686,7 +8686,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ba004131-9543-4ff6-94df-043957c1ffd6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ba004131-9543-4ff6-94df-043957c1ffd6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9ac30d2b-a698-40b0-9002-e254b38b7d31' class='xr-var-data-in' type='checkbox'><label for='data-9ac30d2b-a698-40b0-9002-e254b38b7d31' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ac60d35c-f105-49b0-898c-4a8f52d14302' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ac60d35c-f105-49b0-898c-4a8f52d14302' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-53f1057e-a709-469e-a339-80ad7917bd20' class='xr-var-data-in' type='checkbox'><label for='data-53f1057e-a709-469e-a339-80ad7917bd20' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8742,7 +8742,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-3b8f3724-6b90-4697-8ce5-68bfc1012113' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3b8f3724-6b90-4697-8ce5-68bfc1012113' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-378e474e-ddcf-4dfc-aa18-6bc7701a437c' class='xr-var-data-in' type='checkbox'><label for='data-378e474e-ddcf-4dfc-aa18-6bc7701a437c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b7766d83-26f7-445b-97b8-62badd8863b4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b7766d83-26f7-445b-97b8-62badd8863b4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cabe9d42-3600-4a62-99ae-e0107b622ee0' class='xr-var-data-in' type='checkbox'><label for='data-cabe9d42-3600-4a62-99ae-e0107b622ee0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8798,7 +8798,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-66a2aab8-f44d-4d4b-9f67-fe398476cd86' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-66a2aab8-f44d-4d4b-9f67-fe398476cd86' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6fcae1a1-a287-42ca-ad86-601ab2258555' class='xr-var-data-in' type='checkbox'><label for='data-6fcae1a1-a287-42ca-ad86-601ab2258555' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-2713d9c6-bbb4-4682-997e-3e98fd74ae57' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2713d9c6-bbb4-4682-997e-3e98fd74ae57' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-03ec8e61-788d-434a-b7c9-b9d3fed6ba90' class='xr-var-data-in' type='checkbox'><label for='data-03ec8e61-788d-434a-b7c9-b9d3fed6ba90' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8854,7 +8854,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-06196276-2a51-4d40-b3d1-9400822af19c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-06196276-2a51-4d40-b3d1-9400822af19c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d218c735-f7b3-4da8-b13e-176971f8d57b' class='xr-var-data-in' type='checkbox'><label for='data-d218c735-f7b3-4da8-b13e-176971f8d57b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-fe03dcd8-f1c9-44be-8ece-d4bd690ad672' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-fe03dcd8-f1c9-44be-8ece-d4bd690ad672' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3dbacac7-3c89-4d8d-bd51-e6e8096e082c' class='xr-var-data-in' type='checkbox'><label for='data-3dbacac7-3c89-4d8d-bd51-e6e8096e082c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
 corresponding to the number of non-missing occurrences of each allele.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -8911,7 +8911,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b248f068-ddc0-4a8f-8f7e-584d48897f67' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b248f068-ddc0-4a8f-8f7e-584d48897f67' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e0eacd9c-1b92-456c-a502-232dcde356d4' class='xr-var-data-in' type='checkbox'><label for='data-e0eacd9c-1b92-456c-a502-232dcde356d4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-e538f5dc-191a-4121-9f63-87e324e5e97e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e538f5dc-191a-4121-9f63-87e324e5e97e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6a7c33ca-a53f-4b62-b63f-b3441941778d' class='xr-var-data-in' type='checkbox'><label for='data-6a7c33ca-a53f-4b62-b63f-b3441941778d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -8967,7 +8967,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-b2bb0e5f-cf0d-44df-8316-64da98ddf41d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b2bb0e5f-cf0d-44df-8316-64da98ddf41d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d9570bed-50bc-4678-af38-32ecd7d108f5' class='xr-var-data-in' type='checkbox'><label for='data-d9570bed-50bc-4678-af38-32ecd7d108f5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-1d269417-5aa0-49d5-b54f-6f804c6563fd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1d269417-5aa0-49d5-b54f-6f804c6563fd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a21d4063-fb13-4665-a94c-8aee49d20277' class='xr-var-data-in' type='checkbox'><label for='data-a21d4063-fb13-4665-a94c-8aee49d20277' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9023,7 +9023,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-39d2c33c-09a9-4fb2-8664-00e0f4cf806a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-39d2c33c-09a9-4fb2-8664-00e0f4cf806a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c733741e-07c4-4623-87e1-ab1d78273497' class='xr-var-data-in' type='checkbox'><label for='data-c733741e-07c4-4623-87e1-ab1d78273497' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-3223ad5f-29b2-4de3-a2d6-192db5ced494' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3223ad5f-29b2-4de3-a2d6-192db5ced494' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-90807f5f-f03e-46bc-843f-abbfcabdb005' class='xr-var-data-in' type='checkbox'><label for='data-90807f5f-f03e-46bc-843f-abbfcabdb005' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9078,7 +9078,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-789c086a-0506-408f-8047-7893c5717a58' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-789c086a-0506-408f-8047-7893c5717a58' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-431b6d2e-aab5-48ba-a8bc-b7b8d8ce3d9d' class='xr-var-data-in' type='checkbox'><label for='data-431b6d2e-aab5-48ba-a8bc-b7b8d8ce3d9d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-aa2c97fd-06a9-44b7-8734-32c56d1a4d64' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-aa2c97fd-06a9-44b7-8734-32c56d1a4d64' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-19f80228-656a-499b-872e-909ecd4aa84b' class='xr-var-data-in' type='checkbox'><label for='data-19f80228-656a-499b-872e-909ecd4aa84b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9133,7 +9133,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-35853eb4-7c0a-49fa-b6f5-22799969dddc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-35853eb4-7c0a-49fa-b6f5-22799969dddc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6636318e-f76e-4767-99e6-b0c701f28b3f' class='xr-var-data-in' type='checkbox'><label for='data-6636318e-f76e-4767-99e6-b0c701f28b3f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-d61de6f2-dab6-439c-a00d-e0156bfadfd9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d61de6f2-dab6-439c-a00d-e0156bfadfd9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fdd72afa-ba4f-46ae-8f89-1fcddea3d633' class='xr-var-data-in' type='checkbox'><label for='data-fdd72afa-ba4f-46ae-8f89-1fcddea3d633' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9188,7 +9188,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-268b3531-7e3c-47ee-b2d4-689507e81590' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-268b3531-7e3c-47ee-b2d4-689507e81590' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ae4d0e6e-7b18-460f-8c79-f42fe8c43c7c' class='xr-var-data-in' type='checkbox'><label for='data-ae4d0e6e-7b18-460f-8c79-f42fe8c43c7c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-978f6e94-e2b2-401d-abf8-f374cdff3ca0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-978f6e94-e2b2-401d-abf8-f374cdff3ca0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ebc63c19-04c2-4566-b396-1105d662aa2f' class='xr-var-data-in' type='checkbox'><label for='data-ebc63c19-04c2-4566-b396-1105d662aa2f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9243,7 +9243,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-15d4365c-aef3-4835-b054-aac62bf61a9f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-15d4365c-aef3-4835-b054-aac62bf61a9f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bbd58b81-ccf3-47b6-827b-fc82077f06c7' class='xr-var-data-in' type='checkbox'><label for='data-bbd58b81-ccf3-47b6-827b-fc82077f06c7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-6559f914-4906-4a39-ab41-f87cb8dbb3a0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6559f914-4906-4a39-ab41-f87cb8dbb3a0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9a07bd6d-c0bc-4937-bda6-f87fa76c6744' class='xr-var-data-in' type='checkbox'><label for='data-9a07bd6d-c0bc-4937-bda6-f87fa76c6744' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9298,7 +9298,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-5ee9a6c8-906a-46a0-a017-f436f5e84821' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5ee9a6c8-906a-46a0-a017-f436f5e84821' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-25641d59-4d82-4c92-a837-38879eeb765d' class='xr-var-data-in' type='checkbox'><label for='data-25641d59-4d82-4c92-a837-38879eeb765d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-984dc1ac-63ad-4ca0-9cbd-fcfcb3ffa0b5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-984dc1ac-63ad-4ca0-9cbd-fcfcb3ffa0b5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b796cd59-79e6-4870-9ba7-fb41be1da741' class='xr-var-data-in' type='checkbox'><label for='data-b796cd59-79e6-4870-9ba7-fb41be1da741' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9353,7 +9353,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-b9fd2062-6f17-4ee7-a462-8d1c134b7c0f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b9fd2062-6f17-4ee7-a462-8d1c134b7c0f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-72cca314-1a29-4885-985e-07315b13bcbc' class='xr-var-data-in' type='checkbox'><label for='data-72cca314-1a29-4885-985e-07315b13bcbc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-ac16c718-7f3d-42ae-ad59-b5f7aba2c547' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ac16c718-7f3d-42ae-ad59-b5f7aba2c547' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8245fef3-ffcb-4cfd-87f3-64418d8ab25e' class='xr-var-data-in' type='checkbox'><label for='data-8245fef3-ffcb-4cfd-87f3-64418d8ab25e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9433,7 +9433,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-aa9d72bd-db96-4840-956f-7241639fcc64' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-aa9d72bd-db96-4840-956f-7241639fcc64' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f063b6c-1564-446a-b55b-004f07ff01e2' class='xr-var-data-in' type='checkbox'><label for='data-9f063b6c-1564-446a-b55b-004f07ff01e2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-394d4b04-f9d8-435f-b61d-07c1ebab1401' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-394d4b04-f9d8-435f-b61d-07c1ebab1401' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c3be8a4c-cb92-4c10-a799-0192fe97ff95' class='xr-var-data-in' type='checkbox'><label for='data-c3be8a4c-cb92-4c10-a799-0192fe97ff95' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9489,7 +9489,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-8596f3d5-42e7-4351-b755-da02625e4ec1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8596f3d5-42e7-4351-b755-da02625e4ec1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f22c4385-d26e-4c56-8f55-cb71025a5111' class='xr-var-data-in' type='checkbox'><label for='data-f22c4385-d26e-4c56-8f55-cb71025a5111' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-09b0cdcc-9ca3-42be-a98c-654378e95f01' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-09b0cdcc-9ca3-42be-a98c-654378e95f01' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-426db320-d276-4899-84cf-437314374355' class='xr-var-data-in' type='checkbox'><label for='data-426db320-d276-4899-84cf-437314374355' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9545,7 +9545,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-9cb62dce-656e-4f1d-a94a-776a36045d58' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9cb62dce-656e-4f1d-a94a-776a36045d58' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1a225bdc-d44c-4bfa-838b-3ac2c27e920d' class='xr-var-data-in' type='checkbox'><label for='data-1a225bdc-d44c-4bfa-838b-3ac2c27e920d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-e2494842-0cb9-43cc-a703-690e67674f3d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e2494842-0cb9-43cc-a703-690e67674f3d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e8b678e3-1985-4340-965d-6ebc6cb0d31a' class='xr-var-data-in' type='checkbox'><label for='data-e8b678e3-1985-4340-965d-6ebc6cb0d31a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
 the first allele, 2 for the second allele), -1 to indicate a
 missing value, or -2 to indicate a non allele in mixed ploidy datasets.</dd><dt><span>mixed_ploidy :</span></dt><dd>False</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -9627,7 +9627,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-eeeaaad9-8232-46c5-8bf5-e79f734a775d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-eeeaaad9-8232-46c5-8bf5-e79f734a775d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d7173799-f062-400d-ad82-120fbc710dce' class='xr-var-data-in' type='checkbox'><label for='data-d7173799-f062-400d-ad82-120fbc710dce' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-d1fac127-5bff-429e-8d29-cc41b1573ed4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d1fac127-5bff-429e-8d29-cc41b1573ed4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-204a82ad-6c29-4270-b0ab-be8f0201927c' class='xr-var-data-in' type='checkbox'><label for='data-204a82ad-6c29-4270-b0ab-be8f0201927c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9707,7 +9707,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-b27eb61b-ad59-4240-8627-6c81b205e821' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b27eb61b-ad59-4240-8627-6c81b205e821' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-677022ed-af66-4039-9567-8cd58b033d60' class='xr-var-data-in' type='checkbox'><label for='data-677022ed-af66-4039-9567-8cd58b033d60' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-b92eb73f-d9ca-424a-b61e-05c3b838823f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b92eb73f-d9ca-424a-b61e-05c3b838823f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1b881f5d-4352-4eab-8e99-b9c5c01d8c9f' class='xr-var-data-in' type='checkbox'><label for='data-1b881f5d-4352-4eab-8e99-b9c5c01d8c9f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
 all calls are unphased.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -9764,7 +9764,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-13c27468-7af5-4b4f-82ff-350888c7821f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-13c27468-7af5-4b4f-82ff-350888c7821f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ed311fdd-f26b-4dba-a0d7-1fea00a01bb5' class='xr-var-data-in' type='checkbox'><label for='data-ed311fdd-f26b-4dba-a0d7-1fea00a01bb5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-4a94e4ea-48d9-46f0-936f-2bf84e4dfc12' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4a94e4ea-48d9-46f0-936f-2bf84e4dfc12' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3be7585e-5841-4634-8fff-b1cd0e45263a' class='xr-var-data-in' type='checkbox'><label for='data-3be7585e-5841-4634-8fff-b1cd0e45263a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9819,7 +9819,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-fb896d65-6466-49c6-8ddf-fc8bd8f913fc' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fb896d65-6466-49c6-8ddf-fc8bd8f913fc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e2a9cb0f-35d7-4f3d-afa6-7fdf033e0ec5' class='xr-var-data-in' type='checkbox'><label for='data-e2a9cb0f-35d7-4f3d-afa6-7fdf033e0ec5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-f965d77d-96b8-40db-954f-1266a5ce8d52' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f965d77d-96b8-40db-954f-1266a5ce8d52' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7eeec992-53bd-457c-9296-ef274709c396' class='xr-var-data-in' type='checkbox'><label for='data-7eeec992-53bd-457c-9296-ef274709c396' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9874,7 +9874,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-b1d6d99b-1948-4649-a02a-76ac12320cc6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b1d6d99b-1948-4649-a02a-76ac12320cc6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b57100b2-4a6a-44e2-b019-cd85a928aa3a' class='xr-var-data-in' type='checkbox'><label for='data-b57100b2-4a6a-44e2-b019-cd85a928aa3a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-b5761a94-a0d4-4032-bb3e-bcbf0d5ba65f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b5761a94-a0d4-4032-bb3e-bcbf0d5ba65f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-504a02c3-3f56-43e8-b5c3-3a001a6e6d1a' class='xr-var-data-in' type='checkbox'><label for='data-504a02c3-3f56-43e8-b5c3-3a001a6e6d1a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9929,7 +9929,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-df93a07b-459b-4b88-a73a-3f5e32b3d64e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-df93a07b-459b-4b88-a73a-3f5e32b3d64e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5767a0d5-fdf4-4c95-95ba-fb5ef1cc1753' class='xr-var-data-in' type='checkbox'><label for='data-5767a0d5-fdf4-4c95-95ba-fb5ef1cc1753' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-9039873e-a05d-4425-b592-96c6889faf7d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9039873e-a05d-4425-b592-96c6889faf7d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-09c5cdaf-4460-43fb-840e-718f19e84ce0' class='xr-var-data-in' type='checkbox'><label for='data-09c5cdaf-4460-43fb-840e-718f19e84ce0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -9985,7 +9985,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b7aa640c-6b53-41d6-a290-ad5b53a76354' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b7aa640c-6b53-41d6-a290-ad5b53a76354' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-45a5ef99-6617-44bf-b170-6c5980be6538' class='xr-var-data-in' type='checkbox'><label for='data-45a5ef99-6617-44bf-b170-6c5980be6538' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-1082c6c7-1c5a-43a2-8fa9-3940a7760ad4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1082c6c7-1c5a-43a2-8fa9-3940a7760ad4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ebb59569-7157-4f83-8241-d26294847095' class='xr-var-data-in' type='checkbox'><label for='data-ebb59569-7157-4f83-8241-d26294847095' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -10043,7 +10043,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-c6809ad8-8ca5-4a34-9f38-723a9775b0ff' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c6809ad8-8ca5-4a34-9f38-723a9775b0ff' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f874704-1b09-44b3-ad4f-c4beeb4d6156' class='xr-var-data-in' type='checkbox'><label for='data-9f874704-1b09-44b3-ad4f-c4beeb4d6156' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-7a799395-fd6f-40b3-81a5-c8ae1d766137' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7a799395-fd6f-40b3-81a5-c8ae1d766137' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-98df6fe7-5001-450d-88f9-a3e0e9cb6e7b' class='xr-var-data-in' type='checkbox'><label for='data-98df6fe7-5001-450d-88f9-a3e0e9cb6e7b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10099,7 +10099,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-df39c0a7-f7b8-41d9-a98e-13b2f44710d2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-df39c0a7-f7b8-41d9-a98e-13b2f44710d2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5da80a25-464a-4a3b-98a7-9b5fc6f0ddc3' class='xr-var-data-in' type='checkbox'><label for='data-5da80a25-464a-4a3b-98a7-9b5fc6f0ddc3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-70d0f586-d30c-443b-a994-a63dcfff87ae' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-70d0f586-d30c-443b-a994-a63dcfff87ae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b8cf330a-8e7d-4fb3-baba-ad66cbfd472e' class='xr-var-data-in' type='checkbox'><label for='data-b8cf330a-8e7d-4fb3-baba-ad66cbfd472e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10155,7 +10155,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-8f9c5f33-57be-48af-9e6e-afbf1a2f60f7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8f9c5f33-57be-48af-9e6e-afbf1a2f60f7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4cfcca4d-b7fb-4cd6-9030-1a54be45f67a' class='xr-var-data-in' type='checkbox'><label for='data-4cfcca4d-b7fb-4cd6-9030-1a54be45f67a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-85f6e5b7-46d1-42eb-ab8e-7a7bfb7b014c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-85f6e5b7-46d1-42eb-ab8e-7a7bfb7b014c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-05325850-99d2-45e5-92ad-b2d93ccdd9e3' class='xr-var-data-in' type='checkbox'><label for='data-05325850-99d2-45e5-92ad-b2d93ccdd9e3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10211,7 +10211,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-fd83202f-c0ea-46f5-b83b-0d1f9e4e6702' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-fd83202f-c0ea-46f5-b83b-0d1f9e4e6702' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0e666b8c-bb26-4786-99d6-b27a63decffd' class='xr-var-data-in' type='checkbox'><label for='data-0e666b8c-bb26-4786-99d6-b27a63decffd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-07dbae92-aba3-4f77-aaeb-8b0eed8f3c98' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-07dbae92-aba3-4f77-aaeb-8b0eed8f3c98' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-df8b9759-4998-4ddc-a195-cc9e43605fd9' class='xr-var-data-in' type='checkbox'><label for='data-df8b9759-4998-4ddc-a195-cc9e43605fd9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10267,7 +10267,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-34fbcc87-f3e7-41a6-948a-7aa3cc0170c9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-34fbcc87-f3e7-41a6-948a-7aa3cc0170c9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a5a95a1e-c1d4-41ec-a90f-cd1686cb2cd6' class='xr-var-data-in' type='checkbox'><label for='data-a5a95a1e-c1d4-41ec-a90f-cd1686cb2cd6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-3fd60d4e-af66-4fca-ac24-e833d34f1749' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3fd60d4e-af66-4fca-ac24-e833d34f1749' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ff9d1725-5e2c-495b-bcac-aa957ace28d4' class='xr-var-data-in' type='checkbox'><label for='data-ff9d1725-5e2c-495b-bcac-aa957ace28d4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10323,7 +10323,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-e58bb3fe-25fd-4d5c-a13b-bcc5808baa42' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e58bb3fe-25fd-4d5c-a13b-bcc5808baa42' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3c1a3623-43c0-42ed-8afd-02243d72e98b' class='xr-var-data-in' type='checkbox'><label for='data-3c1a3623-43c0-42ed-8afd-02243d72e98b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-9ee5c637-3eb0-41dc-aa64-b6f0373b31c2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9ee5c637-3eb0-41dc-aa64-b6f0373b31c2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-aab6beb8-2dfb-419f-ab43-beab0855480a' class='xr-var-data-in' type='checkbox'><label for='data-aab6beb8-2dfb-419f-ab43-beab0855480a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10379,7 +10379,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-d8f48193-8e03-446d-9529-2727fa048bd9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d8f48193-8e03-446d-9529-2727fa048bd9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6e090b81-873f-4539-91a0-dc5e519b5a07' class='xr-var-data-in' type='checkbox'><label for='data-6e090b81-873f-4539-91a0-dc5e519b5a07' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-41bb0270-53cf-4cb2-8c92-0fd8a4c5e8b8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-41bb0270-53cf-4cb2-8c92-0fd8a4c5e8b8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4ea65ace-bae4-4a10-8100-72fba6698285' class='xr-var-data-in' type='checkbox'><label for='data-4ea65ace-bae4-4a10-8100-72fba6698285' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
        &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;,
        &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;GBR&#x27;, &#x27;CLM&#x27;,
@@ -10406,7 +10406,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;LWK&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;,
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-c987a9fd-d9e0-401c-90a6-c4d2b69c229f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c987a9fd-d9e0-401c-90a6-c4d2b69c229f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2175c18e-bbdc-4306-ba07-59c6a927d3c6' class='xr-var-data-in' type='checkbox'><label for='data-2175c18e-bbdc-4306-ba07-59c6a927d3c6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-67dc5d26-f8fd-46d9-bd2b-b05bf6e8e401' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-67dc5d26-f8fd-46d9-bd2b-b05bf6e8e401' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-05772e9f-3202-48d3-84c6-1d10d291d465' class='xr-var-data-in' type='checkbox'><label for='data-05772e9f-3202-48d3-84c6-1d10d291d465' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;EUR&#x27;, &#x27;AMR&#x27;,
@@ -10433,7 +10433,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-b5f5f1d4-60ac-46fb-9c16-301f9bfcb2f1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b5f5f1d4-60ac-46fb-9c16-301f9bfcb2f1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-29480d96-df4d-473f-91f1-1b28cc5aa67e' class='xr-var-data-in' type='checkbox'><label for='data-29480d96-df4d-473f-91f1-1b28cc5aa67e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-5f776856-69c3-41fb-a0d8-3658ddadba3a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5f776856-69c3-41fb-a0d8-3658ddadba3a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e087be9c-d45e-47cb-affe-5c49e0d926df' class='xr-var-data-in' type='checkbox'><label for='data-e087be9c-d45e-47cb-affe-5c49e0d926df' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
        False, False,  True, False,  True, False, False, False,  True,
         True,  True, False,  True,  True, False,  True,  True, False,
        False,  True, False,  True, False,  True,  True, False,  True,
@@ -10460,7 +10460,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
         True, False,  True, False,  True, False,  True, False, False,
         True, False, False,  True, False,  True,  True,  True, False,
         True, False,  True, False, False,  True,  True,  True,  True,
-        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-d484ba80-6e8e-40e7-ade5-4189d23cd1f7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d484ba80-6e8e-40e7-ade5-4189d23cd1f7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cba49400-b819-4b21-91f2-a519e8018b0e' class='xr-var-data-in' type='checkbox'><label for='data-cba49400-b819-4b21-91f2-a519e8018b0e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
+        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-70924ea0-370e-4e5a-aea0-2af66659013e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-70924ea0-370e-4e5a-aea0-2af66659013e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-924870da-8da9-44e1-872f-634fe8e363df' class='xr-var-data-in' type='checkbox'><label for='data-924870da-8da9-44e1-872f-634fe8e363df' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
         True, False, False,  True,  True,  True,  True,  True,  True,
         True, False,  True,  True, False, False, False, False, False,
         True, False,  True,  True,  True, False,  True, False,  True,
@@ -10487,7 +10487,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        False,  True,  True, False, False, False, False,  True, False,
         True, False,  True,  True, False, False, False, False,  True,
         True,  True,  True,  True,  True, False, False,  True, False,
-       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-2d02788a-3f44-42cb-9cf5-16d0ca6c72f3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2d02788a-3f44-42cb-9cf5-16d0ca6c72f3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf00fdda-c97d-4dea-8fdc-827585bf20a9' class='xr-var-data-in' type='checkbox'><label for='data-bf00fdda-c97d-4dea-8fdc-827585bf20a9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
+       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-9ae57c40-2e68-4cff-9155-b99a72a192aa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9ae57c40-2e68-4cff-9155-b99a72a192aa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b2c710a7-f06f-4674-9779-ff03f3462d34' class='xr-var-data-in' type='checkbox'><label for='data-b2c710a7-f06f-4674-9779-ff03f3462d34' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
        5, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5, 5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5,
        5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4, 6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5,
        4, 4, 5, 8, 3, 4, 4, 7, 5, 2, 6, 7, 6, 5, 3, 4, 5, 5, 5, 5, 6, 4,
@@ -10498,7 +10498,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
        7, 5, 6, 6, 4, 4, 5, 3, 5, 4, 3, 8, 4, 6, 8, 3, 4, 2, 5, 6, 6, 4,
        3, 5, 7, 4, 5, 5, 6, 3, 2, 4, 5, 6, 7, 2, 4, 2, 1, 5, 3, 4, 9, 6,
        4, 3, 4, 4, 6, 7, 6, 3, 4, 3, 6, 6, 3, 4, 4, 4, 6, 7, 4, 5, 4, 5,
-       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-c5a6f5d0-99c5-4c7b-89d9-a84c5b0fc170' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c5a6f5d0-99c5-4c7b-89d9-a84c5b0fc170' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-983e92ae-3c0d-4605-8ec3-6f90760cf940' class='xr-var-data-in' type='checkbox'><label for='data-983e92ae-3c0d-4605-8ec3-6f90760cf940' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
+       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-877751f4-653e-4822-9fd5-6a3c398dd38a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-877751f4-653e-4822-9fd5-6a3c398dd38a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8253a5d2-2e4a-4302-9a3a-fba947f56212' class='xr-var-data-in' type='checkbox'><label for='data-8253a5d2-2e4a-4302-9a3a-fba947f56212' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -10553,7 +10553,7 @@ <h2>Quality control<a class="headerlink" href="#quality-control" title="Permalin
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-bb5ecd89-08fa-478e-a960-0b4c0821fa1d' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-bb5ecd89-08fa-478e-a960-0b4c0821fa1d' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-c6cfed19-64de-4306-ae88-3fab73d2f4fd' class='xr-section-summary-in' type='checkbox'  ><label for='section-c6cfed19-64de-4306-ae88-3fab73d2f4fd' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-ec9921ff-8413-47b2-b744-03d27ebf279d' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-ec9921ff-8413-47b2-b744-03d27ebf279d' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-e1c7243e-f273-4ce4-8953-b091700528ad' class='xr-section-summary-in' type='checkbox'  ><label for='section-e1c7243e-f273-4ce4-8953-b091700528ad' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -11070,7 +11070,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
     PurpleHair                (samples) bool 250B False False ... True True
     CaffeineConsumption       (samples) int64 2kB 4 4 4 3 6 2 2 ... 4 6 4 6 5 5
     sample_dp_mean            (samples) float64 2kB dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;
-Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-a3c84ef2-0c6d-4606-98ec-d392b5dd4f07' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-a3c84ef2-0c6d-4606-98ec-d392b5dd4f07' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-95861723-b082-4fa5-88e8-d3f9b5680447' class='xr-section-summary-in' type='checkbox'  checked><label for='section-95861723-b082-4fa5-88e8-d3f9b5680447' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-ce96f037-0971-4de2-94c2-5ec52d05b414' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ce96f037-0971-4de2-94c2-5ec52d05b414' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fac1f120-a84e-41cb-8b7c-e043cf582798' class='xr-var-data-in' type='checkbox'><label for='data-fac1f120-a84e-41cb-8b7c-e043cf582798' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-3aae24ef-cc24-4932-bee5-90de320a08fe' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3aae24ef-cc24-4932-bee5-90de320a08fe' class='xr-section-summary' >Data variables: <span>(41)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ba0e2657-5fa3-4d5c-9546-49bdb8d3b167' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ba0e2657-5fa3-4d5c-9546-49bdb8d3b167' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b61400ae-cd35-40ef-88f8-1beafbb34ea9' class='xr-var-data-in' type='checkbox'><label for='data-b61400ae-cd35-40ef-88f8-1beafbb34ea9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
+Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-4b4fe142-7435-4cfd-a6e9-eca270a8f97e' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-4b4fe142-7435-4cfd-a6e9-eca270a8f97e' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 10879</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-2a4ca3bc-47d1-4001-a7d9-4eaed5d2cec3' class='xr-section-summary-in' type='checkbox'  checked><label for='section-2a4ca3bc-47d1-4001-a7d9-4eaed5d2cec3' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-31bf17e5-b55f-47fc-9610-f1460ecf6715' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-31bf17e5-b55f-47fc-9610-f1460ecf6715' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-110a9003-bb86-4d55-b7bd-aa7a0bc0f7c9' class='xr-var-data-in' type='checkbox'><label for='data-110a9003-bb86-4d55-b7bd-aa7a0bc0f7c9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e16c71ea-8081-460a-9b33-a628b3aa5c08' class='xr-section-summary-in' type='checkbox'  checked><label for='section-e16c71ea-8081-460a-9b33-a628b3aa5c08' class='xr-section-summary' >Data variables: <span>(41)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-60daae86-9ea0-4a07-8e6e-32001f980373' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-60daae86-9ea0-4a07-8e6e-32001f980373' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5880463c-73a7-43dc-bd96-771a500f042c' class='xr-var-data-in' type='checkbox'><label for='data-5880463c-73a7-43dc-bd96-771a500f042c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11126,7 +11126,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 3), meta=np.ndarray&gt;</div><input id='attrs-4f61f0fc-b12d-4cb4-9f04-5a99ef26fff3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-4f61f0fc-b12d-4cb4-9f04-5a99ef26fff3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1e33f909-45be-444d-80e0-ae7d0a2e6f93' class='xr-var-data-in' type='checkbox'><label for='data-1e33f909-45be-444d-80e0-ae7d0a2e6f93' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 3), meta=np.ndarray&gt;</div><input id='attrs-79ad74da-2812-4007-bcb3-b97b41e08bdc' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-79ad74da-2812-4007-bcb3-b97b41e08bdc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-86c6c0a3-ecc2-49f8-a78c-778e421cfd27' class='xr-var-data-in' type='checkbox'><label for='data-86c6c0a3-ecc2-49f8-a78c-778e421cfd27' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
 Counts are sorted following the ordering defined in the VCF specification.
 
 - For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``
@@ -11190,7 +11190,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-e2f236aa-62b8-44a4-9c8c-5c6e4940b3d2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e2f236aa-62b8-44a4-9c8c-5c6e4940b3d2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-737ce4df-ba31-4933-a49d-a8f5f0fd8803' class='xr-var-data-in' type='checkbox'><label for='data-737ce4df-ba31-4933-a49d-a8f5f0fd8803' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-0d83c9f0-a28a-41ca-b946-bbd5bbcb0766' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0d83c9f0-a28a-41ca-b946-bbd5bbcb0766' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b41d70dc-74ce-4e08-919c-d62105ca2f22' class='xr-var-data-in' type='checkbox'><label for='data-b41d70dc-74ce-4e08-919c-d62105ca2f22' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
 ploidy and alleles dimensions. The ordering of genotype strings follows the
 ordering outlined in the VCF specification for arrays of size &quot;G&quot;.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -11247,7 +11247,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d114730d-830e-4e36-8d8e-8aa18526ae16' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d114730d-830e-4e36-8d8e-8aa18526ae16' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-489f47f9-c284-4fcd-9029-2b73f09284ea' class='xr-var-data-in' type='checkbox'><label for='data-489f47f9-c284-4fcd-9029-2b73f09284ea' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-6ee1d86d-23ee-4860-a26b-2c9b085d2673' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6ee1d86d-23ee-4860-a26b-2c9b085d2673' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-239add6d-a200-4256-8f50-81c5fd70aae5' class='xr-var-data-in' type='checkbox'><label for='data-239add6d-a200-4256-8f50-81c5fd70aae5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11303,7 +11303,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-2a3d8d86-5d42-412f-994b-db9e56144d62' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2a3d8d86-5d42-412f-994b-db9e56144d62' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fd306287-6397-4972-9327-cbb0224b4de3' class='xr-var-data-in' type='checkbox'><label for='data-fd306287-6397-4972-9327-cbb0224b4de3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-f47e6529-6cc2-44ec-9fb1-faeb1bbe71f0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f47e6529-6cc2-44ec-9fb1-faeb1bbe71f0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-afee9527-3190-4f95-9f3d-4ba5de9f4553' class='xr-var-data-in' type='checkbox'><label for='data-afee9527-3190-4f95-9f3d-4ba5de9f4553' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11359,7 +11359,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-4f581316-53b6-4101-ae27-322fe2a34415' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4f581316-53b6-4101-ae27-322fe2a34415' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4d95f3e3-a811-40f9-8ddf-da72316d6da2' class='xr-var-data-in' type='checkbox'><label for='data-4d95f3e3-a811-40f9-8ddf-da72316d6da2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-15336fa0-4df2-4530-9bd3-5ddd180940e1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-15336fa0-4df2-4530-9bd3-5ddd180940e1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c2e9e38c-9d31-400d-8b8c-e00edd835161' class='xr-var-data-in' type='checkbox'><label for='data-c2e9e38c-9d31-400d-8b8c-e00edd835161' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11415,7 +11415,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-dfc675ce-0e9d-4154-9e98-b04b267d69b4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dfc675ce-0e9d-4154-9e98-b04b267d69b4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-330bad03-fb71-4ac4-8a9f-e6d40a505fa4' class='xr-var-data-in' type='checkbox'><label for='data-330bad03-fb71-4ac4-8a9f-e6d40a505fa4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-ae5e270c-9758-4296-b79a-d6966c42c02f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ae5e270c-9758-4296-b79a-d6966c42c02f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-04630b9d-228e-436f-9164-4ef720131a3e' class='xr-var-data-in' type='checkbox'><label for='data-04630b9d-228e-436f-9164-4ef720131a3e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11471,7 +11471,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d79484f9-63c6-4640-bfa4-cea5fbd4924a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d79484f9-63c6-4640-bfa4-cea5fbd4924a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-33009ba9-fb5b-420b-8982-6d8ec2d736a4' class='xr-var-data-in' type='checkbox'><label for='data-33009ba9-fb5b-420b-8982-6d8ec2d736a4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-4b25e712-8fb9-4d03-bc03-86e8d16ef5b3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4b25e712-8fb9-4d03-bc03-86e8d16ef5b3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-affe16f1-b6b4-45d6-8c47-b5560f4802ce' class='xr-var-data-in' type='checkbox'><label for='data-affe16f1-b6b4-45d6-8c47-b5560f4802ce' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11527,7 +11527,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-93c42ba9-6c30-4474-b563-df5f5762bc1a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-93c42ba9-6c30-4474-b563-df5f5762bc1a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f5ea71c-8931-4cb1-aff1-b2c0ce3a387e' class='xr-var-data-in' type='checkbox'><label for='data-9f5ea71c-8931-4cb1-aff1-b2c0ce3a387e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-e653fcfa-bf26-465c-a47f-b5580f959814' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e653fcfa-bf26-465c-a47f-b5580f959814' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f6a67ebd-5ec3-4ba2-b1b0-5b80eae46b05' class='xr-var-data-in' type='checkbox'><label for='data-f6a67ebd-5ec3-4ba2-b1b0-5b80eae46b05' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11583,7 +11583,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-0627950f-d844-4d16-a162-22aa2bd1a3a8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0627950f-d844-4d16-a162-22aa2bd1a3a8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d265b248-d0d4-42ce-8741-c50bf16fcabb' class='xr-var-data-in' type='checkbox'><label for='data-d265b248-d0d4-42ce-8741-c50bf16fcabb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-29b00e92-2272-4649-99e4-5af09c3ef0f5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-29b00e92-2272-4649-99e4-5af09c3ef0f5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9c0a3ad4-f7b2-4353-868d-8c6126346df3' class='xr-var-data-in' type='checkbox'><label for='data-9c0a3ad4-f7b2-4353-868d-8c6126346df3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
 corresponding to the number of non-missing occurrences of each allele.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -11640,7 +11640,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-fae0992f-bd88-4e88-85ff-a838799a19a7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fae0992f-bd88-4e88-85ff-a838799a19a7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8043a8f9-c210-4837-8737-e948b38a7021' class='xr-var-data-in' type='checkbox'><label for='data-8043a8f9-c210-4837-8737-e948b38a7021' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-6464eff9-f771-43bd-a8dc-1ada5f59ef80' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6464eff9-f771-43bd-a8dc-1ada5f59ef80' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8915b3f0-0f75-4c9f-b93c-bfbc634f5a9b' class='xr-var-data-in' type='checkbox'><label for='data-8915b3f0-0f75-4c9f-b93c-bfbc634f5a9b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11696,7 +11696,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-0868e3d0-28b5-4e0c-8cd6-c4d25cd9063c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0868e3d0-28b5-4e0c-8cd6-c4d25cd9063c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c11d3e28-e141-485c-9d6d-59baedec18f9' class='xr-var-data-in' type='checkbox'><label for='data-c11d3e28-e141-485c-9d6d-59baedec18f9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-a557e988-7795-4156-9497-69e341e5b22e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a557e988-7795-4156-9497-69e341e5b22e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cf1f338a-681c-443e-bcc3-b5aaf72dbd89' class='xr-var-data-in' type='checkbox'><label for='data-cf1f338a-681c-443e-bcc3-b5aaf72dbd89' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11752,7 +11752,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-523a64f8-d51d-4814-b295-4332193343a4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-523a64f8-d51d-4814-b295-4332193343a4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c9fca17d-2772-436d-81d7-777f02e38e0f' class='xr-var-data-in' type='checkbox'><label for='data-c9fca17d-2772-436d-81d7-777f02e38e0f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-d9e89aef-b600-49f2-95e5-0c73673c33d7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d9e89aef-b600-49f2-95e5-0c73673c33d7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b574bd49-2059-4da2-b517-29138acb81d6' class='xr-var-data-in' type='checkbox'><label for='data-b574bd49-2059-4da2-b517-29138acb81d6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11807,7 +11807,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-abdb07dc-c613-4bb2-9d98-8cbe9bc2584d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-abdb07dc-c613-4bb2-9d98-8cbe9bc2584d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-46180844-49fb-4809-97c3-352c1024dfd3' class='xr-var-data-in' type='checkbox'><label for='data-46180844-49fb-4809-97c3-352c1024dfd3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-1c3e42e6-06a8-49e6-bec4-0a09ec51e2db' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1c3e42e6-06a8-49e6-bec4-0a09ec51e2db' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8d18371f-f25a-4ef1-b304-70dd2a1feef0' class='xr-var-data-in' type='checkbox'><label for='data-8d18371f-f25a-4ef1-b304-70dd2a1feef0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11862,7 +11862,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-8bb15772-2bbc-4b12-9720-13d5146686e7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8bb15772-2bbc-4b12-9720-13d5146686e7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bf1921ce-1db6-435c-9305-b6b4a755e0ef' class='xr-var-data-in' type='checkbox'><label for='data-bf1921ce-1db6-435c-9305-b6b4a755e0ef' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-9878d1a7-debd-44fa-a956-77fcddb1dd84' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9878d1a7-debd-44fa-a956-77fcddb1dd84' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b2f21393-bbf8-4a51-a01d-61a4249294ad' class='xr-var-data-in' type='checkbox'><label for='data-b2f21393-bbf8-4a51-a01d-61a4249294ad' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11917,7 +11917,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-9f79f5c2-f6f2-44b4-b0b4-ef0b9f7ae845' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9f79f5c2-f6f2-44b4-b0b4-ef0b9f7ae845' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bc8438e0-8afd-4925-bf41-c1bd24f8bc9a' class='xr-var-data-in' type='checkbox'><label for='data-bc8438e0-8afd-4925-bf41-c1bd24f8bc9a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-c5880f95-e0f2-49d3-a8d7-7561bba8ced9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c5880f95-e0f2-49d3-a8d7-7561bba8ced9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-48506dbe-e547-4258-8ade-e79988da25ca' class='xr-var-data-in' type='checkbox'><label for='data-48506dbe-e547-4258-8ade-e79988da25ca' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -11972,7 +11972,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-253d2813-acce-45b4-9a4d-0e0330126a48' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-253d2813-acce-45b4-9a4d-0e0330126a48' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-859a8a6c-3a17-4fbc-96d7-714c0208d2ed' class='xr-var-data-in' type='checkbox'><label for='data-859a8a6c-3a17-4fbc-96d7-714c0208d2ed' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-0ca554e9-3b01-4f99-87b5-9fffb95af467' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0ca554e9-3b01-4f99-87b5-9fffb95af467' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5de630f9-f88b-4530-b19d-d9770aca51fb' class='xr-var-data-in' type='checkbox'><label for='data-5de630f9-f88b-4530-b19d-d9770aca51fb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12027,7 +12027,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-33bca307-d253-4ba8-94f9-073655721e42' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-33bca307-d253-4ba8-94f9-073655721e42' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f94ce4e1-3d41-42c5-9011-4e4eab59eb85' class='xr-var-data-in' type='checkbox'><label for='data-f94ce4e1-3d41-42c5-9011-4e4eab59eb85' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-773dc1c2-aa0f-429b-8b1a-44b374778ebe' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-773dc1c2-aa0f-429b-8b1a-44b374778ebe' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a3062c94-d420-4677-b8c2-cd369d100a0e' class='xr-var-data-in' type='checkbox'><label for='data-a3062c94-d420-4677-b8c2-cd369d100a0e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12082,7 +12082,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-43491e8f-39b8-4344-a8e4-2f07b6fef1ed' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-43491e8f-39b8-4344-a8e4-2f07b6fef1ed' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-aad1e274-9d81-4ac5-b8ae-34ec9db5a66a' class='xr-var-data-in' type='checkbox'><label for='data-aad1e274-9d81-4ac5-b8ae-34ec9db5a66a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-a29e69f6-730b-4af7-8d34-86383bdeb484' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a29e69f6-730b-4af7-8d34-86383bdeb484' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-086bcd90-ff14-404e-9b31-da42c8e79547' class='xr-var-data-in' type='checkbox'><label for='data-086bcd90-ff14-404e-9b31-da42c8e79547' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12162,7 +12162,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-ceebac54-6726-4eda-9152-3dcc51cde4a7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ceebac54-6726-4eda-9152-3dcc51cde4a7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7406ff46-76c0-4fa3-97e9-dde773bd958c' class='xr-var-data-in' type='checkbox'><label for='data-7406ff46-76c0-4fa3-97e9-dde773bd958c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-275badb6-d739-41ed-baf9-61ec457955ac' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-275badb6-d739-41ed-baf9-61ec457955ac' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cde53206-08e1-497d-b957-4381e153ef4a' class='xr-var-data-in' type='checkbox'><label for='data-cde53206-08e1-497d-b957-4381e153ef4a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12218,7 +12218,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-977bf0fe-dba8-44cf-a2ea-4143af88eec0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-977bf0fe-dba8-44cf-a2ea-4143af88eec0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-88d3c500-047e-437b-b271-9f32aeed8c38' class='xr-var-data-in' type='checkbox'><label for='data-88d3c500-047e-437b-b271-9f32aeed8c38' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-9a336d23-ce57-4406-af1b-bac0bf3c010f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9a336d23-ce57-4406-af1b-bac0bf3c010f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-66b4bd69-760a-4b1d-a4bd-1a713e9658e9' class='xr-var-data-in' type='checkbox'><label for='data-66b4bd69-760a-4b1d-a4bd-1a713e9658e9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12274,7 +12274,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-9636c288-d48b-46d5-a200-27b1be04b8c2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9636c288-d48b-46d5-a200-27b1be04b8c2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ffdab016-947f-4a7e-9c6d-d1331480bcca' class='xr-var-data-in' type='checkbox'><label for='data-ffdab016-947f-4a7e-9c6d-d1331480bcca' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-5854b8f1-f29c-4493-b53e-6c5e131919ac' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5854b8f1-f29c-4493-b53e-6c5e131919ac' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6a89c28c-f230-49a6-ad74-accfc3b0b64a' class='xr-var-data-in' type='checkbox'><label for='data-6a89c28c-f230-49a6-ad74-accfc3b0b64a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
 the first allele, 2 for the second allele), -1 to indicate a
 missing value, or -2 to indicate a non allele in mixed ploidy datasets.</dd><dt><span>mixed_ploidy :</span></dt><dd>False</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -12356,7 +12356,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-0cfe2ca0-33a4-4a39-80f3-a817baca105a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0cfe2ca0-33a4-4a39-80f3-a817baca105a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-75f083f2-502b-4264-a10c-2a1bc3cc4f63' class='xr-var-data-in' type='checkbox'><label for='data-75f083f2-502b-4264-a10c-2a1bc3cc4f63' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-29003cbf-f8a9-4535-8d0a-14ad9589770d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-29003cbf-f8a9-4535-8d0a-14ad9589770d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-839c5fc8-2cda-4ee8-91c7-6b433bd78562' class='xr-var-data-in' type='checkbox'><label for='data-839c5fc8-2cda-4ee8-91c7-6b433bd78562' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12436,7 +12436,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-c962119c-bcdf-47c8-9210-c6a4c289fd8a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c962119c-bcdf-47c8-9210-c6a4c289fd8a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6d8dcb1b-53e8-40ce-b2be-2a2e614d7c9c' class='xr-var-data-in' type='checkbox'><label for='data-6d8dcb1b-53e8-40ce-b2be-2a2e614d7c9c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 250), meta=np.ndarray&gt;</div><input id='attrs-3db2300e-baf7-4485-aeb9-129b73cec0be' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3db2300e-baf7-4485-aeb9-129b73cec0be' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ce34b230-565e-4e25-bac7-3d93d37e660f' class='xr-var-data-in' type='checkbox'><label for='data-ce34b230-565e-4e25-bac7-3d93d37e660f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
 all calls are unphased.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -12493,7 +12493,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-d5dd58f7-28ba-4bc2-9af2-1a1a800891f4' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d5dd58f7-28ba-4bc2-9af2-1a1a800891f4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-11b83a44-1498-4b41-a959-83e2b5f73ec6' class='xr-var-data-in' type='checkbox'><label for='data-11b83a44-1498-4b41-a959-83e2b5f73ec6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-e6cbb4f2-39d9-4132-990e-df569a8e1941' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e6cbb4f2-39d9-4132-990e-df569a8e1941' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ae292697-2a8f-45d5-864f-7c39eb60b2b8' class='xr-var-data-in' type='checkbox'><label for='data-ae292697-2a8f-45d5-864f-7c39eb60b2b8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12548,7 +12548,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-67cdc478-476f-4029-adc3-95d5d7748caa' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-67cdc478-476f-4029-adc3-95d5d7748caa' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3fcdda4b-7f55-4faa-9e43-8a2d03f7da73' class='xr-var-data-in' type='checkbox'><label for='data-3fcdda4b-7f55-4faa-9e43-8a2d03f7da73' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-c0701469-34be-4985-8494-ce75be816406' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c0701469-34be-4985-8494-ce75be816406' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f1d66828-a0d9-4a20-a7ff-2fe0a22a8ad1' class='xr-var-data-in' type='checkbox'><label for='data-f1d66828-a0d9-4a20-a7ff-2fe0a22a8ad1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12603,7 +12603,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-72b50480-0873-4d88-a204-5fb13124c73a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-72b50480-0873-4d88-a204-5fb13124c73a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-10b703bd-554b-49cf-9c4c-e7238ed7e066' class='xr-var-data-in' type='checkbox'><label for='data-10b703bd-554b-49cf-9c4c-e7238ed7e066' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-3fc89bfc-85f2-42a9-852f-c7cc9ed25e9d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3fc89bfc-85f2-42a9-852f-c7cc9ed25e9d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-671a2913-a6f2-4dcc-9b43-dea9aaadac00' class='xr-var-data-in' type='checkbox'><label for='data-671a2913-a6f2-4dcc-9b43-dea9aaadac00' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12658,7 +12658,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-361699fe-b08f-41a2-ac1f-7be87570282c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-361699fe-b08f-41a2-ac1f-7be87570282c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f9f442db-8452-4399-8605-306dc6d2ed8d' class='xr-var-data-in' type='checkbox'><label for='data-f9f442db-8452-4399-8605-306dc6d2ed8d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 2), meta=np.ndarray&gt;</div><input id='attrs-f36e362f-de5b-4171-8663-5d78fb87ab16' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f36e362f-de5b-4171-8663-5d78fb87ab16' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d11809be-803e-4ba3-b4bb-97ba9eb49b84' class='xr-var-data-in' type='checkbox'><label for='data-d11809be-803e-4ba3-b4bb-97ba9eb49b84' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12714,7 +12714,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-10ad6574-f4f2-490c-9c46-51467b4768bc' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-10ad6574-f4f2-490c-9c46-51467b4768bc' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-00a8d13d-8617-4cac-a3c5-8af1c74b7088' class='xr-var-data-in' type='checkbox'><label for='data-00a8d13d-8617-4cac-a3c5-8af1c74b7088' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-52917923-7ac5-4a2e-b328-c7d2df0d01d7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-52917923-7ac5-4a2e-b328-c7d2df0d01d7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6c9645e6-70e9-41e1-a453-1f05d617c2a6' class='xr-var-data-in' type='checkbox'><label for='data-6c9645e6-70e9-41e1-a453-1f05d617c2a6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -12772,7 +12772,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-563e78d4-7bbb-47b1-aaaa-c717d23263f4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-563e78d4-7bbb-47b1-aaaa-c717d23263f4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9f7e9d1a-8ccb-4127-b23f-fdd8d343bcff' class='xr-var-data-in' type='checkbox'><label for='data-9f7e9d1a-8ccb-4127-b23f-fdd8d343bcff' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000, 1), meta=np.ndarray&gt;</div><input id='attrs-0c240b31-0b32-4826-8a94-dc97279f5ecf' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0c240b31-0b32-4826-8a94-dc97279f5ecf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-88f42893-64a8-4aa7-b2de-90f981daf29f' class='xr-var-data-in' type='checkbox'><label for='data-88f42893-64a8-4aa7-b2de-90f981daf29f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12828,7 +12828,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-1a7a5c1d-ebdf-4824-b27e-c92683bc192a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1a7a5c1d-ebdf-4824-b27e-c92683bc192a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a5a2c85c-3bfc-4b15-9626-f1f10c9fe496' class='xr-var-data-in' type='checkbox'><label for='data-a5a2c85c-3bfc-4b15-9626-f1f10c9fe496' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-3350cea5-9cd4-4099-be59-05fe15acbf05' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3350cea5-9cd4-4099-be59-05fe15acbf05' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-090329e5-bad2-4577-8223-0ad7e5d4277e' class='xr-var-data-in' type='checkbox'><label for='data-090329e5-bad2-4577-8223-0ad7e5d4277e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12884,7 +12884,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-39dc438e-e2cd-4b9c-816e-51e1c972a603' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-39dc438e-e2cd-4b9c-816e-51e1c972a603' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ef156f80-09b8-43c2-8bf6-dc6c6d8e7529' class='xr-var-data-in' type='checkbox'><label for='data-ef156f80-09b8-43c2-8bf6-dc6c6d8e7529' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-8bb576bb-9f2b-44eb-8900-b38e3ced115c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8bb576bb-9f2b-44eb-8900-b38e3ced115c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0aede0dc-e1f5-4f89-913c-ed5d547d396c' class='xr-var-data-in' type='checkbox'><label for='data-0aede0dc-e1f5-4f89-913c-ed5d547d396c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12940,7 +12940,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d4d382e6-bcbb-4270-af0e-471014c20633' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d4d382e6-bcbb-4270-af0e-471014c20633' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cd2519bc-60ef-4e3e-aeb7-e1beedef6728' class='xr-var-data-in' type='checkbox'><label for='data-cd2519bc-60ef-4e3e-aeb7-e1beedef6728' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-8166e175-a9ad-4eea-a1cd-e6dfb6ee996c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8166e175-a9ad-4eea-a1cd-e6dfb6ee996c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3db4d4f0-a048-432d-a62d-ae0ef395f246' class='xr-var-data-in' type='checkbox'><label for='data-3db4d4f0-a048-432d-a62d-ae0ef395f246' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -12996,7 +12996,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-6cc2e793-662f-47ef-9792-f0ac0619bf80' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6cc2e793-662f-47ef-9792-f0ac0619bf80' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f369134d-8997-4a9d-bd12-6136e22551af' class='xr-var-data-in' type='checkbox'><label for='data-f369134d-8997-4a9d-bd12-6136e22551af' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-d891bb6a-18f2-4117-be93-e8da288df19b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d891bb6a-18f2-4117-be93-e8da288df19b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-64c18514-3fbb-4d3a-ae47-e2a2b73a4c8f' class='xr-var-data-in' type='checkbox'><label for='data-64c18514-3fbb-4d3a-ae47-e2a2b73a4c8f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13052,7 +13052,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-b8b7d935-7eaf-45ef-8475-9c52d8b6e299' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b8b7d935-7eaf-45ef-8475-9c52d8b6e299' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2551a004-2324-4980-ad6f-d2510c75cd96' class='xr-var-data-in' type='checkbox'><label for='data-2551a004-2324-4980-ad6f-d2510c75cd96' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10000,), meta=np.ndarray&gt;</div><input id='attrs-49e3081c-e8dc-4ddc-8159-bfba8da95634' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-49e3081c-e8dc-4ddc-8159-bfba8da95634' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c7a186f7-748c-42cd-8842-68d594062595' class='xr-var-data-in' type='checkbox'><label for='data-c7a186f7-748c-42cd-8842-68d594062595' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13108,7 +13108,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-db1e7c58-72d7-4838-8b7f-3aa1e56489ea' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-db1e7c58-72d7-4838-8b7f-3aa1e56489ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-979f0f7f-4421-47e2-ae2b-92c7e5afed7c' class='xr-var-data-in' type='checkbox'><label for='data-979f0f7f-4421-47e2-ae2b-92c7e5afed7c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-97a74c39-faf2-48da-bda5-ef99244509ae' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-97a74c39-faf2-48da-bda5-ef99244509ae' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-436f259d-5992-47a5-9a7d-8fde50b82c0e' class='xr-var-data-in' type='checkbox'><label for='data-436f259d-5992-47a5-9a7d-8fde50b82c0e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
        &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;,
        &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;GBR&#x27;, &#x27;CLM&#x27;,
@@ -13135,7 +13135,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        &#x27;LWK&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;,
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-d61b980a-5651-475e-8e4c-124d96de2459' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d61b980a-5651-475e-8e4c-124d96de2459' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c57e47a-27a0-4888-a9ba-c37f3b008eea' class='xr-var-data-in' type='checkbox'><label for='data-5c57e47a-27a0-4888-a9ba-c37f3b008eea' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-cfcf5213-88c2-42a1-a49f-0c386644cdc6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cfcf5213-88c2-42a1-a49f-0c386644cdc6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fd5d4d05-1e4f-4336-bde6-c297a28934fb' class='xr-var-data-in' type='checkbox'><label for='data-fd5d4d05-1e4f-4336-bde6-c297a28934fb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;EUR&#x27;, &#x27;AMR&#x27;,
@@ -13162,7 +13162,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-886e4ba7-4e53-4134-b332-768c5d8535c9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-886e4ba7-4e53-4134-b332-768c5d8535c9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a8d22339-29b8-42b3-8fbc-2bad6614947f' class='xr-var-data-in' type='checkbox'><label for='data-a8d22339-29b8-42b3-8fbc-2bad6614947f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-af250208-7545-44ef-9907-bdd672f3184d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-af250208-7545-44ef-9907-bdd672f3184d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-117fd69d-135c-4f15-adac-b1eaa1cd5138' class='xr-var-data-in' type='checkbox'><label for='data-117fd69d-135c-4f15-adac-b1eaa1cd5138' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
        False, False,  True, False,  True, False, False, False,  True,
         True,  True, False,  True,  True, False,  True,  True, False,
        False,  True, False,  True, False,  True,  True, False,  True,
@@ -13189,7 +13189,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
         True, False,  True, False,  True, False,  True, False, False,
         True, False, False,  True, False,  True,  True,  True, False,
         True, False,  True, False, False,  True,  True,  True,  True,
-        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-3bf90d35-2e50-4633-8ff2-e8837d735ee8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3bf90d35-2e50-4633-8ff2-e8837d735ee8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d2c19d0d-5751-43af-871d-eacd06d9db1a' class='xr-var-data-in' type='checkbox'><label for='data-d2c19d0d-5751-43af-871d-eacd06d9db1a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
+        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-5526f41a-5667-479c-a544-c04656406110' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5526f41a-5667-479c-a544-c04656406110' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-aa074754-cc62-4c03-aacb-d24fdcc2b6b5' class='xr-var-data-in' type='checkbox'><label for='data-aa074754-cc62-4c03-aacb-d24fdcc2b6b5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
         True, False, False,  True,  True,  True,  True,  True,  True,
         True, False,  True,  True, False, False, False, False, False,
         True, False,  True,  True,  True, False,  True, False,  True,
@@ -13216,7 +13216,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        False,  True,  True, False, False, False, False,  True, False,
         True, False,  True,  True, False, False, False, False,  True,
         True,  True,  True,  True,  True, False, False,  True, False,
-       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-f5fd3dbf-9f59-4310-90df-af874271dde5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f5fd3dbf-9f59-4310-90df-af874271dde5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b9528f87-2920-4305-b39e-abe6f41e745d' class='xr-var-data-in' type='checkbox'><label for='data-b9528f87-2920-4305-b39e-abe6f41e745d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
+       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-32d89b7f-7fa8-4a68-8d05-90ac347cf3ef' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-32d89b7f-7fa8-4a68-8d05-90ac347cf3ef' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-70b05cf9-0495-4e32-a71a-7923fb65cc53' class='xr-var-data-in' type='checkbox'><label for='data-70b05cf9-0495-4e32-a71a-7923fb65cc53' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
        5, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5, 5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5,
        5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4, 6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5,
        4, 4, 5, 8, 3, 4, 4, 7, 5, 2, 6, 7, 6, 5, 3, 4, 5, 5, 5, 5, 6, 4,
@@ -13227,7 +13227,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        7, 5, 6, 6, 4, 4, 5, 3, 5, 4, 3, 8, 4, 6, 8, 3, 4, 2, 5, 6, 6, 4,
        3, 5, 7, 4, 5, 5, 6, 3, 2, 4, 5, 6, 7, 2, 4, 2, 1, 5, 3, 4, 9, 6,
        4, 3, 4, 4, 6, 7, 6, 3, 4, 3, 6, 6, 3, 4, 4, 4, 6, 7, 4, 5, 4, 5,
-       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-9acd1d41-fee2-4f30-889f-5d0fa2eb0be7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9acd1d41-fee2-4f30-889f-5d0fa2eb0be7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-18a81ddc-c9ff-44d2-8c11-624615880f55' class='xr-var-data-in' type='checkbox'><label for='data-18a81ddc-c9ff-44d2-8c11-624615880f55' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
+       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-d7d14105-c7e4-4a16-ace5-f4178a2dad94' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d7d14105-c7e4-4a16-ace5-f4178a2dad94' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-04c0e115-e1d1-4e49-bfc4-726808daa26a' class='xr-var-data-in' type='checkbox'><label for='data-04c0e115-e1d1-4e49-bfc4-726808daa26a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13282,7 +13282,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-0709c3ac-83cf-4c06-89a3-ccca966f0f2a' class='xr-section-summary-in' type='checkbox'  ><label for='section-0709c3ac-83cf-4c06-89a3-ccca966f0f2a' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-4acdf590-e8fe-4a9c-b1ce-cae1917113e4' class='xr-index-data-in' type='checkbox'/><label for='index-4acdf590-e8fe-4a9c-b1ce-cae1917113e4' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-feb4d996-a881-4ae1-a95a-d7480b5e6dd9' class='xr-section-summary-in' type='checkbox'  ><label for='section-feb4d996-a881-4ae1-a95a-d7480b5e6dd9' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-16729e50-0565-4dfe-aa02-853eea8d2fdc' class='xr-section-summary-in' type='checkbox'  ><label for='section-16729e50-0565-4dfe-aa02-853eea8d2fdc' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-54c10cfd-51d7-4df6-8658-18df51546e81' class='xr-index-data-in' type='checkbox'/><label for='index-54c10cfd-51d7-4df6-8658-18df51546e81' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-99d690f9-9aed-4f31-97ad-00d5301ef8ba' class='xr-section-summary-in' type='checkbox'  ><label for='section-99d690f9-9aed-4f31-97ad-00d5301ef8ba' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -13812,7 +13812,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
     CaffeineConsumption       (samples) int64 2kB 4 4 4 3 6 2 2 ... 4 6 4 6 5 5
     sample_dp_mean            (samples) float64 2kB dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;
     call_dosage               (variants, samples) int64 17MB dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;
-Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-307c607e-c7a7-4fa3-8e35-da779c776d57' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-307c607e-c7a7-4fa3-8e35-da779c776d57' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 8394</li><li><span>traits</span>: 1</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-4c1b5ce5-564c-43a6-8d84-a4a3c5c52e63' class='xr-section-summary-in' type='checkbox'  checked><label for='section-4c1b5ce5-564c-43a6-8d84-a4a3c5c52e63' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-b39ac2cb-4d14-43e0-ae86-d2bf3926866c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b39ac2cb-4d14-43e0-ae86-d2bf3926866c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e00f60c5-1bf0-4117-b21f-03cc57332eb7' class='xr-var-data-in' type='checkbox'><label for='data-e00f60c5-1bf0-4117-b21f-03cc57332eb7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-d642456c-4ccd-4c26-80a7-7d8f443a73e5' class='xr-section-summary-in' type='checkbox'  checked><label for='section-d642456c-4ccd-4c26-80a7-7d8f443a73e5' class='xr-section-summary' >Data variables: <span>(45)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_beta</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-24f6e4c0-b790-4d54-a7ea-bac168959899' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-24f6e4c0-b790-4d54-a7ea-bac168959899' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-139b8df3-3281-4253-8eeb-fd0ff36154bf' class='xr-var-data-in' type='checkbox'><label for='data-139b8df3-3281-4253-8eeb-fd0ff36154bf' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Beta values associated with each variant and trait.</dd></dl></div><div class='xr-var-data'><table>
+Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-d57293bd-8ec6-4d11-ac06-60585a02fb22' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-d57293bd-8ec6-4d11-ac06-60585a02fb22' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>variants</span>: 8394</li><li><span>traits</span>: 1</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>samples</span>: 250</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-37af413f-734a-48b2-8d68-ee2d2eb2fac2' class='xr-section-summary-in' type='checkbox'  checked><label for='section-37af413f-734a-48b2-8d68-ee2d2eb2fac2' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-395a844b-1bef-493d-8ac3-b5cc8f050744' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-395a844b-1bef-493d-8ac3-b5cc8f050744' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7bebea25-1ff3-49dc-848b-2e03211236ae' class='xr-var-data-in' type='checkbox'><label for='data-7bebea25-1ff3-49dc-848b-2e03211236ae' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-ed5ee6ee-307f-4067-8aeb-ab26ec727e2c' class='xr-section-summary-in' type='checkbox'  checked><label for='section-ed5ee6ee-307f-4067-8aeb-ab26ec727e2c' class='xr-section-summary' >Data variables: <span>(45)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_beta</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-38d11e86-b533-4687-b22a-71c8bc77967b' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-38d11e86-b533-4687-b22a-71c8bc77967b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-add15717-e779-48e1-a291-76778fd23ba7' class='xr-var-data-in' type='checkbox'><label for='data-add15717-e779-48e1-a291-76778fd23ba7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Beta values associated with each variant and trait.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13868,7 +13868,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_t_value</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-5602eba3-8977-4473-8dbd-eacf117ec649' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5602eba3-8977-4473-8dbd-eacf117ec649' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3d5dc021-54a0-476c-a082-9d3bd1c92b86' class='xr-var-data-in' type='checkbox'><label for='data-3d5dc021-54a0-476c-a082-9d3bd1c92b86' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>T statistics for each beta.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_t_value</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-63c7b036-7611-475d-a25f-3fb9a82bd629' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-63c7b036-7611-475d-a25f-3fb9a82bd629' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7a3647e0-6a93-459a-877b-ac67b715eda5' class='xr-var-data-in' type='checkbox'><label for='data-7a3647e0-6a93-459a-877b-ac67b715eda5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>T statistics for each beta.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13924,7 +13924,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_p_value</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-e45e0aaa-8fe2-467b-95ef-3f085cee04fd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e45e0aaa-8fe2-467b-95ef-3f085cee04fd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9daa3211-b67e-4755-ac9f-733de6e499e3' class='xr-var-data-in' type='checkbox'><label for='data-9daa3211-b67e-4755-ac9f-733de6e499e3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_linreg_p_value</span></div><div class='xr-var-dims'>(variants, traits)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-ee571db5-a564-4a86-93ee-0d0688c2297c' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ee571db5-a564-4a86-93ee-0d0688c2297c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b4d59617-26c4-4f6e-9b52-dc7abcb217e7' class='xr-var-data-in' type='checkbox'><label for='data-b4d59617-26c4-4f6e-9b52-dc7abcb217e7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -13980,7 +13980,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-5a0d3edc-85bf-4095-bfe6-c7079c505063' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-5a0d3edc-85bf-4095-bfe6-c7079c505063' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3540c1e4-b208-443b-8861-2d67900d346f' class='xr-var-data-in' type='checkbox'><label for='data-3540c1e4-b208-443b-8861-2d67900d346f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-53aa82b5-81a9-4080-ab13-15c750cfc88d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-53aa82b5-81a9-4080-ab13-15c750cfc88d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1d2b35cf-66c4-49b7-bee3-c57448d7dc32' class='xr-var-data-in' type='checkbox'><label for='data-1d2b35cf-66c4-49b7-bee3-c57448d7dc32' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14036,7 +14036,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 3), meta=np.ndarray&gt;</div><input id='attrs-1e6de432-e890-4caf-a14c-1263d597faa8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1e6de432-e890-4caf-a14c-1263d597faa8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-86064cb8-52f2-4a5d-857b-6c9c3104e3a3' class='xr-var-data-in' type='checkbox'><label for='data-86064cb8-52f2-4a5d-857b-6c9c3104e3a3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 3), meta=np.ndarray&gt;</div><input id='attrs-90eeebe3-8cc0-46e8-bfec-f99aa1c15fad' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-90eeebe3-8cc0-46e8-bfec-f99aa1c15fad' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a7388bca-fa4b-4f86-a1e7-8bbe723fd2dd' class='xr-var-data-in' type='checkbox'><label for='data-a7388bca-fa4b-4f86-a1e7-8bbe723fd2dd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
 Counts are sorted following the ordering defined in the VCF specification.
 
 - For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``
@@ -14100,7 +14100,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-77becf86-2253-4c9d-996d-eecbac572fb8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-77becf86-2253-4c9d-996d-eecbac572fb8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4a541328-383d-4af7-a541-392481e1487c' class='xr-var-data-in' type='checkbox'><label for='data-4a541328-383d-4af7-a541-392481e1487c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-88369ab1-24f5-4440-8097-5e18f67751d2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-88369ab1-24f5-4440-8097-5e18f67751d2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0276bfbd-31bd-4977-b47d-fd30c1e6f707' class='xr-var-data-in' type='checkbox'><label for='data-0276bfbd-31bd-4977-b47d-fd30c1e6f707' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
 ploidy and alleles dimensions. The ordering of genotype strings follows the
 ordering outlined in the VCF specification for arrays of size &quot;G&quot;.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -14157,7 +14157,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-660705fb-a7f4-44e9-9e22-5399b6a49b6a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-660705fb-a7f4-44e9-9e22-5399b6a49b6a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e93d61b8-3b39-4326-bcf6-67680c01094f' class='xr-var-data-in' type='checkbox'><label for='data-e93d61b8-3b39-4326-bcf6-67680c01094f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-75f7c975-a14f-4112-a5dd-6c624fbd1bd6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-75f7c975-a14f-4112-a5dd-6c624fbd1bd6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-97b8a3b1-edff-4617-9673-f1fcd341ccbe' class='xr-var-data-in' type='checkbox'><label for='data-97b8a3b1-edff-4617-9673-f1fcd341ccbe' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14213,7 +14213,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-70e2f5a7-7a6b-4379-8719-d90176e6c936' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-70e2f5a7-7a6b-4379-8719-d90176e6c936' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e772c851-f8d8-48d1-ab55-6205df9422b6' class='xr-var-data-in' type='checkbox'><label for='data-e772c851-f8d8-48d1-ab55-6205df9422b6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-f7fa76e9-9762-4638-b2d9-38f4eb79c2d3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f7fa76e9-9762-4638-b2d9-38f4eb79c2d3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ec670f2f-dbdc-45b7-9e7a-910d6c7fc265' class='xr-var-data-in' type='checkbox'><label for='data-ec670f2f-dbdc-45b7-9e7a-910d6c7fc265' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14269,7 +14269,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-595c523f-bce9-4049-bb53-916f151ae8a1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-595c523f-bce9-4049-bb53-916f151ae8a1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9be263c5-a317-4094-a4e6-fff78624a354' class='xr-var-data-in' type='checkbox'><label for='data-9be263c5-a317-4094-a4e6-fff78624a354' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-f9162390-888d-4452-8f0e-86529a5cd610' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f9162390-888d-4452-8f0e-86529a5cd610' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0fd3f69d-40f4-4b5e-b077-5f84b7c5d1aa' class='xr-var-data-in' type='checkbox'><label for='data-0fd3f69d-40f4-4b5e-b077-5f84b7c5d1aa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14325,7 +14325,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-42f1a769-2bd0-4c99-a68f-9915073cfd29' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-42f1a769-2bd0-4c99-a68f-9915073cfd29' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ebc812a2-e5be-4488-afa1-c9a305eb7891' class='xr-var-data-in' type='checkbox'><label for='data-ebc812a2-e5be-4488-afa1-c9a305eb7891' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-a0111c6e-e3b1-45b4-81d8-268170b9996c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a0111c6e-e3b1-45b4-81d8-268170b9996c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6f2c3b45-75b9-4404-a141-f25d3cb3dc8c' class='xr-var-data-in' type='checkbox'><label for='data-6f2c3b45-75b9-4404-a141-f25d3cb3dc8c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14381,7 +14381,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-ec955a42-b92c-41f3-bc66-11b22a19dd86' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ec955a42-b92c-41f3-bc66-11b22a19dd86' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-73c35431-8c5b-4877-af15-08196bde9579' class='xr-var-data-in' type='checkbox'><label for='data-73c35431-8c5b-4877-af15-08196bde9579' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-50f5a866-f970-468a-ae73-9ec3768a63f8' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-50f5a866-f970-468a-ae73-9ec3768a63f8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f10a49a4-380f-4425-a803-3fde90fa730e' class='xr-var-data-in' type='checkbox'><label for='data-f10a49a4-380f-4425-a803-3fde90fa730e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14437,7 +14437,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-3bf73d9b-70c0-497e-b774-0dc04e1e272b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3bf73d9b-70c0-497e-b774-0dc04e1e272b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-24d21b0b-7c08-4454-baf4-1e64d253c8f8' class='xr-var-data-in' type='checkbox'><label for='data-24d21b0b-7c08-4454-baf4-1e64d253c8f8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-55bfde31-6341-4462-a410-4b1585c1cf28' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-55bfde31-6341-4462-a410-4b1585c1cf28' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-06ddc21c-ac10-4c87-8ebf-19d73a92bd56' class='xr-var-data-in' type='checkbox'><label for='data-06ddc21c-ac10-4c87-8ebf-19d73a92bd56' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14493,7 +14493,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-390d58cf-de12-40a2-b2d5-14a92a4d871d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-390d58cf-de12-40a2-b2d5-14a92a4d871d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0aec15a1-3002-4a55-abf1-729c9086319f' class='xr-var-data-in' type='checkbox'><label for='data-0aec15a1-3002-4a55-abf1-729c9086319f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-e534bd40-8590-4d84-86c2-56140ea224e8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e534bd40-8590-4d84-86c2-56140ea224e8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-38d5c30d-606d-442a-9795-d889e7bf33b9' class='xr-var-data-in' type='checkbox'><label for='data-38d5c30d-606d-442a-9795-d889e7bf33b9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
 corresponding to the number of non-missing occurrences of each allele.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -14550,7 +14550,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-8d595669-3edc-4930-a013-c7ba28ceea70' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8d595669-3edc-4930-a013-c7ba28ceea70' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-20845ae1-2358-4bc5-98e4-76da2825f879' class='xr-var-data-in' type='checkbox'><label for='data-20845ae1-2358-4bc5-98e4-76da2825f879' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-68c828f5-f7d1-4d81-a350-12e329444de6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-68c828f5-f7d1-4d81-a350-12e329444de6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-31846bf9-4c49-4036-9ce1-e8268613c3df' class='xr-var-data-in' type='checkbox'><label for='data-31846bf9-4c49-4036-9ce1-e8268613c3df' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14606,7 +14606,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-b777161e-806a-4643-92fb-94d106992a31' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b777161e-806a-4643-92fb-94d106992a31' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e7731953-1e35-4666-a7a6-2b9f61075efc' class='xr-var-data-in' type='checkbox'><label for='data-e7731953-1e35-4666-a7a6-2b9f61075efc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-52ceee63-64a9-46f8-8365-947d35da3b87' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-52ceee63-64a9-46f8-8365-947d35da3b87' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-18ab2325-bf5b-45a9-ac73-947a1611a711' class='xr-var-data-in' type='checkbox'><label for='data-18ab2325-bf5b-45a9-ac73-947a1611a711' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14662,7 +14662,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-6274896d-3b29-4255-b4f8-a604d7f81965' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6274896d-3b29-4255-b4f8-a604d7f81965' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ff222388-3712-447c-a88d-e694ae1602ae' class='xr-var-data-in' type='checkbox'><label for='data-ff222388-3712-447c-a88d-e694ae1602ae' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-e87376d1-768d-49ce-a814-1b60bad7ec5b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e87376d1-768d-49ce-a814-1b60bad7ec5b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c08c2f91-beab-4e51-9cac-743944d4884c' class='xr-var-data-in' type='checkbox'><label for='data-c08c2f91-beab-4e51-9cac-743944d4884c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14717,7 +14717,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-e385eae0-c228-458c-913a-38021076454a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e385eae0-c228-458c-913a-38021076454a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c14d07e-eb1b-4e1d-8113-3879bdc7a4f9' class='xr-var-data-in' type='checkbox'><label for='data-5c14d07e-eb1b-4e1d-8113-3879bdc7a4f9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-cc2e0ebd-3b63-47c5-9aff-4209cc647996' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cc2e0ebd-3b63-47c5-9aff-4209cc647996' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-561dc62b-d523-4e43-9a63-8eedd69bc003' class='xr-var-data-in' type='checkbox'><label for='data-561dc62b-d523-4e43-9a63-8eedd69bc003' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14772,7 +14772,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-e04f855a-6fa3-411c-b698-8555fd9e4564' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e04f855a-6fa3-411c-b698-8555fd9e4564' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9364caff-7bb9-4eb1-91cc-19b656b5090b' class='xr-var-data-in' type='checkbox'><label for='data-9364caff-7bb9-4eb1-91cc-19b656b5090b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-52dfd127-a42e-4b5b-9ee0-1e641a28dc3f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-52dfd127-a42e-4b5b-9ee0-1e641a28dc3f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1614ebdb-e7cb-4d61-bdfb-cd8bb653a8aa' class='xr-var-data-in' type='checkbox'><label for='data-1614ebdb-e7cb-4d61-bdfb-cd8bb653a8aa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14827,7 +14827,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-f6415008-62a2-4c74-ae21-0e9d22767c5d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f6415008-62a2-4c74-ae21-0e9d22767c5d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4fc618b2-675d-4baf-846c-a8c2d547a9b2' class='xr-var-data-in' type='checkbox'><label for='data-4fc618b2-675d-4baf-846c-a8c2d547a9b2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-ed7b95b2-961f-49b0-8da5-cbd1345c357e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ed7b95b2-961f-49b0-8da5-cbd1345c357e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-81ffecb5-b978-4017-8003-4fed96577968' class='xr-var-data-in' type='checkbox'><label for='data-81ffecb5-b978-4017-8003-4fed96577968' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14882,7 +14882,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-4111b44a-a3fc-4901-81d4-12f725adfe65' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4111b44a-a3fc-4901-81d4-12f725adfe65' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-90c306fb-b038-44f5-86c8-ae214e355d93' class='xr-var-data-in' type='checkbox'><label for='data-90c306fb-b038-44f5-86c8-ae214e355d93' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-acbf4eca-4ac9-494e-9292-953f00daacb0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-acbf4eca-4ac9-494e-9292-953f00daacb0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-71e002d0-34b6-413c-96b8-f84a494ad736' class='xr-var-data-in' type='checkbox'><label for='data-71e002d0-34b6-413c-96b8-f84a494ad736' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14937,7 +14937,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-7da576d9-1090-4e1a-bef4-dc53851ae573' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7da576d9-1090-4e1a-bef4-dc53851ae573' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-68748354-9abe-4b4f-ba35-87ac78dafe3b' class='xr-var-data-in' type='checkbox'><label for='data-68748354-9abe-4b4f-ba35-87ac78dafe3b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-9434db0c-3e7a-40f5-ba07-3d8e44f2b607' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9434db0c-3e7a-40f5-ba07-3d8e44f2b607' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c128bbac-cb7d-4962-bd11-26add67cd77c' class='xr-var-data-in' type='checkbox'><label for='data-c128bbac-cb7d-4962-bd11-26add67cd77c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -14992,7 +14992,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-998b6181-7a93-4a82-b62f-29a68977f1de' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-998b6181-7a93-4a82-b62f-29a68977f1de' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a0f0bbe3-344a-4f14-ba96-01d6c205a6af' class='xr-var-data-in' type='checkbox'><label for='data-a0f0bbe3-344a-4f14-ba96-01d6c205a6af' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-0dc37e99-afc9-48ff-a626-b8c6c9484449' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0dc37e99-afc9-48ff-a626-b8c6c9484449' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8c99b25b-33bc-4d0b-b24a-0459e99f4ff9' class='xr-var-data-in' type='checkbox'><label for='data-8c99b25b-33bc-4d0b-b24a-0459e99f4ff9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15072,7 +15072,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-06833b33-1ab7-4632-a524-7357a4dd6f96' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-06833b33-1ab7-4632-a524-7357a4dd6f96' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2948c532-0ee3-42cb-a870-6d536154ed28' class='xr-var-data-in' type='checkbox'><label for='data-2948c532-0ee3-42cb-a870-6d536154ed28' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-fd716009-1da0-46bd-a1dd-a28574c4a49e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fd716009-1da0-46bd-a1dd-a28574c4a49e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a3796842-89f6-4edf-8135-2d6666adb61b' class='xr-var-data-in' type='checkbox'><label for='data-a3796842-89f6-4edf-8135-2d6666adb61b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15128,7 +15128,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-c727feff-ac5e-4276-b5dd-fafe553f0b9f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c727feff-ac5e-4276-b5dd-fafe553f0b9f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d5c614cb-497d-42a6-94f4-ad66e5cf1fd3' class='xr-var-data-in' type='checkbox'><label for='data-d5c614cb-497d-42a6-94f4-ad66e5cf1fd3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-6fe12f19-e534-4c9a-88c9-44e1739066b0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6fe12f19-e534-4c9a-88c9-44e1739066b0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-25fb5a55-2689-4498-a4e3-930af2cc79c8' class='xr-var-data-in' type='checkbox'><label for='data-25fb5a55-2689-4498-a4e3-930af2cc79c8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15184,7 +15184,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-b0a53262-9ece-4aaa-bdec-5a2ba4b62640' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b0a53262-9ece-4aaa-bdec-5a2ba4b62640' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bc1b9132-eb39-44d2-89ea-b427f7523b4c' class='xr-var-data-in' type='checkbox'><label for='data-bc1b9132-eb39-44d2-89ea-b427f7523b4c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-76b267a2-fdf2-40f6-ad28-affa12f8a0c8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-76b267a2-fdf2-40f6-ad28-affa12f8a0c8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fea8f5ee-d8f8-4a6f-a1d9-0e3ac97133b7' class='xr-var-data-in' type='checkbox'><label for='data-fea8f5ee-d8f8-4a6f-a1d9-0e3ac97133b7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
 the first allele, 2 for the second allele), -1 to indicate a
 missing value, or -2 to indicate a non allele in mixed ploidy datasets.</dd><dt><span>mixed_ploidy :</span></dt><dd>False</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -15266,7 +15266,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-07aab83c-822a-4deb-b96f-39c78cc7abc3' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-07aab83c-822a-4deb-b96f-39c78cc7abc3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-04c3050e-d33b-4851-b219-e691114cd041' class='xr-var-data-in' type='checkbox'><label for='data-04c3050e-d33b-4851-b219-e691114cd041' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-41e01e4a-d09d-438e-adcb-fcbdf491e1f9' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-41e01e4a-d09d-438e-adcb-fcbdf491e1f9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7fe5c54c-91a0-4c0c-8ba5-be40a2724cc2' class='xr-var-data-in' type='checkbox'><label for='data-7fe5c54c-91a0-4c0c-8ba5-be40a2724cc2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15346,7 +15346,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-cee04455-92b0-43a8-a9ec-84534894e3f2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cee04455-92b0-43a8-a9ec-84534894e3f2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5690138d-5093-4509-b7eb-2ca6d538d6b1' class='xr-var-data-in' type='checkbox'><label for='data-5690138d-5093-4509-b7eb-2ca6d538d6b1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-76c0c2f0-b6c5-4795-8852-7aee888b8a7e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-76c0c2f0-b6c5-4795-8852-7aee888b8a7e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-89b7cd33-881f-40c4-8cc0-d7a8cc485971' class='xr-var-data-in' type='checkbox'><label for='data-89b7cd33-881f-40c4-8cc0-d7a8cc485971' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
 all calls are unphased.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -15403,7 +15403,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-ec133107-c167-4ced-8366-017841e9c59f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ec133107-c167-4ced-8366-017841e9c59f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-160230b2-10e6-4c62-a25f-698572140f01' class='xr-var-data-in' type='checkbox'><label for='data-160230b2-10e6-4c62-a25f-698572140f01' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-dd846d43-072c-4669-bd29-7ee5cd48ba8a' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-dd846d43-072c-4669-bd29-7ee5cd48ba8a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2a9a02b0-33df-493c-a8e3-eec0b6f28e5a' class='xr-var-data-in' type='checkbox'><label for='data-2a9a02b0-33df-493c-a8e3-eec0b6f28e5a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15458,7 +15458,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-d678a4c3-fc76-4976-b2ce-3952ab53013a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d678a4c3-fc76-4976-b2ce-3952ab53013a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-06e93594-97fd-4357-a154-a26ead475dae' class='xr-var-data-in' type='checkbox'><label for='data-06e93594-97fd-4357-a154-a26ead475dae' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-fe3b59e9-b48e-47b3-95c1-7f2f7fd88c76' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fe3b59e9-b48e-47b3-95c1-7f2f7fd88c76' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fabf2607-d003-493b-bd8e-c59da98b2f34' class='xr-var-data-in' type='checkbox'><label for='data-fabf2607-d003-493b-bd8e-c59da98b2f34' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15513,7 +15513,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-5841c282-2fb6-41fd-bc67-294eb9e68c3b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5841c282-2fb6-41fd-bc67-294eb9e68c3b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bd082bbf-e037-45ee-bc1b-12b40c3da931' class='xr-var-data-in' type='checkbox'><label for='data-bd082bbf-e037-45ee-bc1b-12b40c3da931' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-3f969399-ba28-41e8-b344-ad8576c9a950' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3f969399-ba28-41e8-b344-ad8576c9a950' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c566f07d-d544-4d10-828d-ccc4fdbb133d' class='xr-var-data-in' type='checkbox'><label for='data-c566f07d-d544-4d10-828d-ccc4fdbb133d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15568,7 +15568,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-6db2c584-22e1-46aa-a979-dbaebe152770' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-6db2c584-22e1-46aa-a979-dbaebe152770' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7d94aba3-5130-4e7b-ab92-7174e1b8fdad' class='xr-var-data-in' type='checkbox'><label for='data-7d94aba3-5130-4e7b-ab92-7174e1b8fdad' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 2), meta=np.ndarray&gt;</div><input id='attrs-9611b698-d104-4fca-bc5d-af3a2ee84de1' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9611b698-d104-4fca-bc5d-af3a2ee84de1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a2f2f5fc-2d11-465c-9984-376a5e603bec' class='xr-var-data-in' type='checkbox'><label for='data-a2f2f5fc-2d11-465c-9984-376a5e603bec' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15624,7 +15624,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-2523de17-ee21-4b9f-a1e6-21a1d2b69f97' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-2523de17-ee21-4b9f-a1e6-21a1d2b69f97' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f512b92f-a5d0-49ed-8795-af941b47c742' class='xr-var-data-in' type='checkbox'><label for='data-f512b92f-a5d0-49ed-8795-af941b47c742' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-a06a144f-dcdc-461e-8d15-e2997fdb2b11' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a06a144f-dcdc-461e-8d15-e2997fdb2b11' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e15956e1-83dd-4970-92d0-fc5ab78ac606' class='xr-var-data-in' type='checkbox'><label for='data-e15956e1-83dd-4970-92d0-fc5ab78ac606' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -15682,7 +15682,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-d8b1e758-ce1d-46dc-a46c-c75c6e5a1afd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d8b1e758-ce1d-46dc-a46c-c75c6e5a1afd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5abec49e-5843-48e4-a20e-bf2047ed58d0' class='xr-var-data-in' type='checkbox'><label for='data-5abec49e-5843-48e4-a20e-bf2047ed58d0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 1), meta=np.ndarray&gt;</div><input id='attrs-137328fe-4eab-487d-b4c8-c6d4eb47528c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-137328fe-4eab-487d-b4c8-c6d4eb47528c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9db61e8a-1015-425a-9995-faecba631972' class='xr-var-data-in' type='checkbox'><label for='data-9db61e8a-1015-425a-9995-faecba631972' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15738,7 +15738,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-e3566404-9f4a-40a8-954d-e96ea4871668' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e3566404-9f4a-40a8-954d-e96ea4871668' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-23734308-524a-4208-8772-91e41290edf6' class='xr-var-data-in' type='checkbox'><label for='data-23734308-524a-4208-8772-91e41290edf6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-20d0f7bd-0f63-4303-8758-c158a1c4f084' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-20d0f7bd-0f63-4303-8758-c158a1c4f084' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8e1d4c1e-245a-4bb8-8220-e3144898e55b' class='xr-var-data-in' type='checkbox'><label for='data-8e1d4c1e-245a-4bb8-8220-e3144898e55b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15794,7 +15794,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-5b35f9cc-91c4-443c-a26e-948ca26b1b9a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5b35f9cc-91c4-443c-a26e-948ca26b1b9a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d52e3ccd-9ab8-44d5-86c9-6738c7e8a465' class='xr-var-data-in' type='checkbox'><label for='data-d52e3ccd-9ab8-44d5-86c9-6738c7e8a465' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-0c073139-1907-487b-a513-68aefd1f4879' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0c073139-1907-487b-a513-68aefd1f4879' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0d04d94f-d092-49b9-b685-b116f8477c0b' class='xr-var-data-in' type='checkbox'><label for='data-0d04d94f-d092-49b9-b685-b116f8477c0b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15850,7 +15850,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-fcf12f6c-3476-4be2-89b9-b5041cc96130' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-fcf12f6c-3476-4be2-89b9-b5041cc96130' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b0ac5c7d-4284-4231-84dd-8c803b63dbb9' class='xr-var-data-in' type='checkbox'><label for='data-b0ac5c7d-4284-4231-84dd-8c803b63dbb9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-a4ed4e83-80ac-4482-946c-f0ec0b2ee298' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a4ed4e83-80ac-4482-946c-f0ec0b2ee298' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-678062fd-d1cc-402a-a31e-e8eb87a5799a' class='xr-var-data-in' type='checkbox'><label for='data-678062fd-d1cc-402a-a31e-e8eb87a5799a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15906,7 +15906,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-896fe58a-ddc0-461f-857d-e2a6519ed75c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-896fe58a-ddc0-461f-857d-e2a6519ed75c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-08ddf411-a061-4f40-a568-97f0895a8c2c' class='xr-var-data-in' type='checkbox'><label for='data-08ddf411-a061-4f40-a568-97f0895a8c2c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-36221c16-e52d-46c0-ae52-14db9d3a31dd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-36221c16-e52d-46c0-ae52-14db9d3a31dd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2b1a699d-f007-4ab7-a18c-019da74d7049' class='xr-var-data-in' type='checkbox'><label for='data-2b1a699d-f007-4ab7-a18c-019da74d7049' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -15962,7 +15962,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-db5ba7d5-9f09-4009-af3f-3d48e5068d32' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-db5ba7d5-9f09-4009-af3f-3d48e5068d32' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7de3e9c9-1c73-43f2-a302-8b3ddd061a31' class='xr-var-data-in' type='checkbox'><label for='data-7de3e9c9-1c73-43f2-a302-8b3ddd061a31' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439,), meta=np.ndarray&gt;</div><input id='attrs-be8961f6-f14d-4717-ab62-8aad35181860' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-be8961f6-f14d-4717-ab62-8aad35181860' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-823b017f-b6ed-44b0-99d4-e1ca4a4da90a' class='xr-var-data-in' type='checkbox'><label for='data-823b017f-b6ed-44b0-99d4-e1ca4a4da90a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16018,7 +16018,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-a65ad6db-0d6b-4637-86f0-45527a67baa5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a65ad6db-0d6b-4637-86f0-45527a67baa5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-536ebcb1-ea6c-45f7-b6f2-507f2b1a0bdb' class='xr-var-data-in' type='checkbox'><label for='data-536ebcb1-ea6c-45f7-b6f2-507f2b1a0bdb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-e6086400-56c4-4a8f-94c4-d5cc733130c2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e6086400-56c4-4a8f-94c4-d5cc733130c2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-87691b15-4a78-497b-a720-75f160b47d1e' class='xr-var-data-in' type='checkbox'><label for='data-87691b15-4a78-497b-a720-75f160b47d1e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
        &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;,
        &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;GBR&#x27;, &#x27;CLM&#x27;,
@@ -16045,7 +16045,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        &#x27;LWK&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;,
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-acf920ba-57fc-40d3-8fb1-a41a033c1d94' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-acf920ba-57fc-40d3-8fb1-a41a033c1d94' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cdacea13-741d-4190-912b-054eed2eff63' class='xr-var-data-in' type='checkbox'><label for='data-cdacea13-741d-4190-912b-054eed2eff63' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-6f0f866d-8886-4a3a-8ff7-7fc469522755' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6f0f866d-8886-4a3a-8ff7-7fc469522755' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0a06d788-ed83-4e43-8471-6b0c95663b0b' class='xr-var-data-in' type='checkbox'><label for='data-0a06d788-ed83-4e43-8471-6b0c95663b0b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;EUR&#x27;, &#x27;AMR&#x27;,
@@ -16072,7 +16072,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-d7bcece4-bd6f-45fc-a788-f4124e12f9f6' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d7bcece4-bd6f-45fc-a788-f4124e12f9f6' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-47cb438a-9eca-4469-ab39-66865da32ead' class='xr-var-data-in' type='checkbox'><label for='data-47cb438a-9eca-4469-ab39-66865da32ead' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-6bfa2253-5ce5-4bba-8b4c-5f81fe51f619' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6bfa2253-5ce5-4bba-8b4c-5f81fe51f619' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2f5fcccb-9ace-452d-953d-0a51c63386fb' class='xr-var-data-in' type='checkbox'><label for='data-2f5fcccb-9ace-452d-953d-0a51c63386fb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
        False, False,  True, False,  True, False, False, False,  True,
         True,  True, False,  True,  True, False,  True,  True, False,
        False,  True, False,  True, False,  True,  True, False,  True,
@@ -16099,7 +16099,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
         True, False,  True, False,  True, False,  True, False, False,
         True, False, False,  True, False,  True,  True,  True, False,
         True, False,  True, False, False,  True,  True,  True,  True,
-        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-5d39e0ff-bf74-46c2-8db9-dac775d6d750' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5d39e0ff-bf74-46c2-8db9-dac775d6d750' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c392dc4d-19ff-49bd-95d0-80fa959fa99b' class='xr-var-data-in' type='checkbox'><label for='data-c392dc4d-19ff-49bd-95d0-80fa959fa99b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
+        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-92e5101d-3320-4937-8e96-b69811f1afc0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-92e5101d-3320-4937-8e96-b69811f1afc0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-600213c0-f33e-47f8-a661-90d164bc2e8d' class='xr-var-data-in' type='checkbox'><label for='data-600213c0-f33e-47f8-a661-90d164bc2e8d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
         True, False, False,  True,  True,  True,  True,  True,  True,
         True, False,  True,  True, False, False, False, False, False,
         True, False,  True,  True,  True, False,  True, False,  True,
@@ -16126,7 +16126,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        False,  True,  True, False, False, False, False,  True, False,
         True, False,  True,  True, False, False, False, False,  True,
         True,  True,  True,  True,  True, False, False,  True, False,
-       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-c6a26ef7-2a37-4d47-a7d4-ed0ae38e25a9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c6a26ef7-2a37-4d47-a7d4-ed0ae38e25a9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-efcbe1bb-c448-46b8-89cd-62875b16c9cb' class='xr-var-data-in' type='checkbox'><label for='data-efcbe1bb-c448-46b8-89cd-62875b16c9cb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
+       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-2ec60d95-a03e-42f4-b6c8-17ba63d05c07' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2ec60d95-a03e-42f4-b6c8-17ba63d05c07' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cb50f7ee-7af8-4e79-bbd4-c3ccb07d3d8e' class='xr-var-data-in' type='checkbox'><label for='data-cb50f7ee-7af8-4e79-bbd4-c3ccb07d3d8e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
        5, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5, 5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5,
        5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4, 6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5,
        4, 4, 5, 8, 3, 4, 4, 7, 5, 2, 6, 7, 6, 5, 3, 4, 5, 5, 5, 5, 6, 4,
@@ -16137,7 +16137,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
        7, 5, 6, 6, 4, 4, 5, 3, 5, 4, 3, 8, 4, 6, 8, 3, 4, 2, 5, 6, 6, 4,
        3, 5, 7, 4, 5, 5, 6, 3, 2, 4, 5, 6, 7, 2, 4, 2, 1, 5, 3, 4, 9, 6,
        4, 3, 4, 4, 6, 7, 6, 3, 4, 3, 6, 6, 3, 4, 4, 4, 6, 7, 4, 5, 4, 5,
-       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-a68f5b51-4150-414e-a362-b0d1e40d27c0' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a68f5b51-4150-414e-a362-b0d1e40d27c0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-8df4aa68-abee-43c8-81a8-e3ef16ed3603' class='xr-var-data-in' type='checkbox'><label for='data-8df4aa68-abee-43c8-81a8-e3ef16ed3603' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
+       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-7d3ef3b1-c56b-4f47-926f-97dc1d55d881' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-7d3ef3b1-c56b-4f47-926f-97dc1d55d881' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-600c5b98-1561-43c5-b1cd-7daff52921fd' class='xr-var-data-in' type='checkbox'><label for='data-600c5b98-1561-43c5-b1cd-7daff52921fd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16192,7 +16192,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-0bdd7fe9-8402-4c46-a94f-68461afb59d1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0bdd7fe9-8402-4c46-a94f-68461afb59d1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2303fab4-e4c6-4b2e-bd57-5c7185d1c98d' class='xr-var-data-in' type='checkbox'><label for='data-2303fab4-e4c6-4b2e-bd57-5c7185d1c98d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(5439, 250), meta=np.ndarray&gt;</div><input id='attrs-77716569-8640-4949-8371-c131b6c2df0f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-77716569-8640-4949-8371-c131b6c2df0f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-57963bfd-c9dc-4d24-9e1e-1b994d2c93c8' class='xr-var-data-in' type='checkbox'><label for='data-57963bfd-c9dc-4d24-9e1e-1b994d2c93c8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16248,7 +16248,7 @@ <h2>Let’s do a GWAS!<a class="headerlink" href="#let-s-do-a-gwas" title="Perma
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-d3c5fcbf-e4b3-48a4-871c-7436af35aa32' class='xr-section-summary-in' type='checkbox'  ><label for='section-d3c5fcbf-e4b3-48a4-871c-7436af35aa32' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-645ef64d-9618-44b1-a786-4f3e4194c56f' class='xr-index-data-in' type='checkbox'/><label for='index-645ef64d-9618-44b1-a786-4f3e4194c56f' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-6aa1ba3b-c416-41be-935f-ce47587f5ae4' class='xr-section-summary-in' type='checkbox'  ><label for='section-6aa1ba3b-c416-41be-935f-ce47587f5ae4' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-acfe89a5-bc66-4455-886d-ce43988ed837' class='xr-section-summary-in' type='checkbox'  ><label for='section-acfe89a5-bc66-4455-886d-ce43988ed837' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-f7fdf0e4-8e23-44cd-b728-29b9c5907f34' class='xr-index-data-in' type='checkbox'/><label for='index-f7fdf0e4-8e23-44cd-b728-29b9c5907f34' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b7c9c7c8-97dd-4bb4-9ccf-4e06d5c5cbfa' class='xr-section-summary-in' type='checkbox'  ><label for='section-b7c9c7c8-97dd-4bb4-9ccf-4e06d5c5cbfa' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
@@ -16900,7 +16900,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
     CaffeineConsumption                  (samples) int64 2kB 4 4 4 3 ... 4 6 5 5
     sample_dp_mean                       (samples) float64 2kB dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;
     call_dosage                          (variants, samples) int64 7MB dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;
-Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-d055a4e1-ec70-4ac0-8a87-fe75397cc192' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-d055a4e1-ec70-4ac0-8a87-fe75397cc192' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 250</li><li><span>components</span>: 10</li><li><span>variants</span>: 3491</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-ef188b95-cedc-4af1-a935-76503e413eca' class='xr-section-summary-in' type='checkbox'  checked><label for='section-ef188b95-cedc-4af1-a935-76503e413eca' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-fb97e89a-e6b3-4c74-ba9d-3cab094e4323' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fb97e89a-e6b3-4c74-ba9d-3cab094e4323' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-af84e268-4e7e-45b7-ac40-0f0acd690298' class='xr-var-data-in' type='checkbox'><label for='data-af84e268-4e7e-45b7-ac40-0f0acd690298' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-20d20cb8-e858-4439-a749-9d8af7909d8b' class='xr-section-summary-in' type='checkbox'  checked><label for='section-20d20cb8-e858-4439-a749-9d8af7909d8b' class='xr-section-summary' >Data variables: <span>(48)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_projection</span></div><div class='xr-var-dims'>(samples, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250, 10), meta=np.ndarray&gt;</div><input id='attrs-7ee85b6b-42b2-42ce-8e87-331de1002b01' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7ee85b6b-42b2-42ce-8e87-331de1002b01' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e9bc6a32-e74a-4476-9406-260c92eff366' class='xr-var-data-in' type='checkbox'><label for='data-e9bc6a32-e74a-4476-9406-260c92eff366' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+Attributes: (7)</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-a4ec0047-0237-4996-957c-d460bd9ff41f' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-a4ec0047-0237-4996-957c-d460bd9ff41f' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span>samples</span>: 250</li><li><span>components</span>: 10</li><li><span>variants</span>: 3491</li><li><span class='xr-has-index'>genotypes</span>: 3</li><li><span>alleles</span>: 2</li><li><span>ploidy</span>: 2</li><li><span>contigs</span>: 84</li><li><span>filters</span>: 1</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-4855663c-f138-455e-88e0-aa45bf95e876' class='xr-section-summary-in' type='checkbox'  checked><label for='section-4855663c-f138-455e-88e0-aa45bf95e876' class='xr-section-summary' >Coordinates: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>genotypes</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>&#x27;0/0&#x27; &#x27;0/1&#x27; &#x27;1/1&#x27;</div><input id='attrs-057f0304-0d8e-4ec4-b410-107ea1edd598' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-057f0304-0d8e-4ec4-b410-107ea1edd598' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-91ff2e71-7218-430c-9c9f-90c94841aad1' class='xr-var-data-in' type='checkbox'><label for='data-91ff2e71-7218-430c-9c9f-90c94841aad1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;&lt;U3&#x27;)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b6ecd952-9a1e-4138-a5c9-e54309e04ef3' class='xr-section-summary-in' type='checkbox'  checked><label for='section-b6ecd952-9a1e-4138-a5c9-e54309e04ef3' class='xr-section-summary' >Data variables: <span>(48)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_projection</span></div><div class='xr-var-dims'>(samples, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250, 10), meta=np.ndarray&gt;</div><input id='attrs-dff728ad-35cc-40f9-a6be-1081f7781c87' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dff728ad-35cc-40f9-a6be-1081f7781c87' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-04d1ce36-b5b0-48f0-a7e9-5fcab0d6c7aa' class='xr-var-data-in' type='checkbox'><label for='data-04d1ce36-b5b0-48f0-a7e9-5fcab0d6c7aa' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -16955,7 +16955,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_component</span></div><div class='xr-var-dims'>(variants, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 10), meta=np.ndarray&gt;</div><input id='attrs-059eadd7-e62c-4df1-b961-33b9fcd39579' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-059eadd7-e62c-4df1-b961-33b9fcd39579' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6de21dd5-8a46-4db4-a7d2-5ad051a47de4' class='xr-var-data-in' type='checkbox'><label for='data-6de21dd5-8a46-4db4-a7d2-5ad051a47de4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_component</span></div><div class='xr-var-dims'>(variants, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 10), meta=np.ndarray&gt;</div><input id='attrs-a8d6cc71-4d6d-4b96-b8f6-9d914cd714d9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a8d6cc71-4d6d-4b96-b8f6-9d914cd714d9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b3fba029-05a9-46cb-aca1-46e5f2247982' class='xr-var-data-in' type='checkbox'><label for='data-b3fba029-05a9-46cb-aca1-46e5f2247982' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17010,7 +17010,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_explained_variance</span></div><div class='xr-var-dims'>(components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10,), meta=np.ndarray&gt;</div><input id='attrs-2648ee75-c606-4ebe-86a8-7a5c178c366c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2648ee75-c606-4ebe-86a8-7a5c178c366c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9dd0420c-a7bb-4e5d-8b4f-2e5e75c59f00' class='xr-var-data-in' type='checkbox'><label for='data-9dd0420c-a7bb-4e5d-8b4f-2e5e75c59f00' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_explained_variance</span></div><div class='xr-var-dims'>(components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10,), meta=np.ndarray&gt;</div><input id='attrs-399d2f9d-0b24-475d-9822-59d7bdbf04c4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-399d2f9d-0b24-475d-9822-59d7bdbf04c4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ee93907d-6266-4511-aa95-6b78036f1c72' class='xr-var-data-in' type='checkbox'><label for='data-ee93907d-6266-4511-aa95-6b78036f1c72' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17065,7 +17065,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_explained_variance_ratio</span></div><div class='xr-var-dims'>(components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10,), meta=np.ndarray&gt;</div><input id='attrs-e4c72893-c43c-429b-a59a-d2addc85065d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e4c72893-c43c-429b-a59a-d2addc85065d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ccd9dc85-2689-40bf-9e9f-a0cfb6266e4d' class='xr-var-data-in' type='checkbox'><label for='data-ccd9dc85-2689-40bf-9e9f-a0cfb6266e4d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_explained_variance_ratio</span></div><div class='xr-var-dims'>(components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(10,), meta=np.ndarray&gt;</div><input id='attrs-75e88323-5c30-43f3-935d-48361ccd10e5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-75e88323-5c30-43f3-935d-48361ccd10e5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-446d87af-1b70-4bdf-bde6-1570e46a7b25' class='xr-var-data-in' type='checkbox'><label for='data-446d87af-1b70-4bdf-bde6-1570e46a7b25' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17120,7 +17120,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_loading</span></div><div class='xr-var-dims'>(variants, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 10), meta=np.ndarray&gt;</div><input id='attrs-709b26e0-d79e-4648-bfab-b307dd543247' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-709b26e0-d79e-4648-bfab-b307dd543247' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6edd88c8-90a8-4fbd-b3be-e39ef1b95cac' class='xr-var-data-in' type='checkbox'><label for='data-6edd88c8-90a8-4fbd-b3be-e39ef1b95cac' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_pca_loading</span></div><div class='xr-var-dims'>(variants, components)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 10), meta=np.ndarray&gt;</div><input id='attrs-d94e235c-000b-4d2b-a01c-f96121c6a8b0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d94e235c-000b-4d2b-a01c-f96121c6a8b0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a6a4e65b-f34c-41f3-a3e1-0a2feabd73e1' class='xr-var-data-in' type='checkbox'><label for='data-a6a4e65b-f34c-41f3-a3e1-0a2feabd73e1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17175,7 +17175,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_alternate_allele_count</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int16</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-22cad587-63b6-42a9-81b4-2ee454553cb0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-22cad587-63b6-42a9-81b4-2ee454553cb0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-75ee40ae-1ecf-4be0-848b-996924fb6035' class='xr-var-data-in' type='checkbox'><label for='data-75ee40ae-1ecf-4be0-848b-996924fb6035' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_alternate_allele_count</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int16</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-ec4b1dc6-3c3f-4577-9b71-e72feb291ec3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ec4b1dc6-3c3f-4577-9b71-e72feb291ec3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1221dafc-6c6b-4c1c-94b1-7ede82dd2233' class='xr-var-data-in' type='checkbox'><label for='data-1221dafc-6c6b-4c1c-94b1-7ede82dd2233' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17230,7 +17230,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-869eabbb-97ff-455a-9c6a-b7b0c2698dbd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-869eabbb-97ff-455a-9c6a-b7b0c2698dbd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b4ce42af-18d2-497d-9898-15d63a753e43' class='xr-var-data-in' type='checkbox'><label for='data-b4ce42af-18d2-497d-9898-15d63a753e43' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_hwe_p_value</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-236ec95c-a180-4a72-86ea-7a205abaca83' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-236ec95c-a180-4a72-86ea-7a205abaca83' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c2f0edc7-a137-4b08-a9ad-8c59785c5817' class='xr-var-data-in' type='checkbox'><label for='data-c2f0edc7-a137-4b08-a9ad-8c59785c5817' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>P values from HWE test for each variant as float in [0, 1].</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17285,7 +17285,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 3), meta=np.ndarray&gt;</div><input id='attrs-19f4d93d-a7f7-4bed-8d72-4325c911a172' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-19f4d93d-a7f7-4bed-8d72-4325c911a172' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1e376082-4f8b-4173-8aab-2844973ce60a' class='xr-var-data-in' type='checkbox'><label for='data-1e376082-4f8b-4173-8aab-2844973ce60a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_genotype_count</span></div><div class='xr-var-dims'>(variants, genotypes)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 3), meta=np.ndarray&gt;</div><input id='attrs-c7536dd1-179c-4220-8f68-9d626dc0ae54' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c7536dd1-179c-4220-8f68-9d626dc0ae54' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-78f7e06b-a9e6-42dc-b6d1-1b15ed746766' class='xr-var-data-in' type='checkbox'><label for='data-78f7e06b-a9e6-42dc-b6d1-1b15ed746766' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The number of observations for each possible genotype at each variant.
 Counts are sorted following the ordering defined in the VCF specification.
 
 - For biallelic, diploid genotypes the ordering is ``00``, ``01``, ``11``
@@ -17348,7 +17348,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-cc1d7c20-8d00-4474-b605-7205c6b815fd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cc1d7c20-8d00-4474-b605-7205c6b815fd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-586182ff-1d6c-4903-b19b-1e5526c519f7' class='xr-var-data-in' type='checkbox'><label for='data-586182ff-1d6c-4903-b19b-1e5526c519f7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>genotype_id</span></div><div class='xr-var-dims'>(genotypes)</div><div class='xr-var-dtype'>&lt;U3</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3,), meta=np.ndarray&gt;</div><input id='attrs-600427e5-9979-4b25-a432-a090f02abdca' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-600427e5-9979-4b25-a432-a090f02abdca' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-33a9a3d9-6c72-47c8-bd23-4e096f3c58ee' class='xr-var-data-in' type='checkbox'><label for='data-33a9a3d9-6c72-47c8-bd23-4e096f3c58ee' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>VCF style genotype strings for all possible genotypes given the size of the
 ploidy and alleles dimensions. The ordering of genotype strings follows the
 ordering outlined in the VCF specification for arrays of size &quot;G&quot;.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -17405,7 +17405,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-36c7c601-38b6-472b-939f-0ee3c9d74073' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-36c7c601-38b6-472b-939f-0ee3c9d74073' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-44cc396c-3d31-49d9-a20a-d659e204418a' class='xr-var-data-in' type='checkbox'><label for='data-44cc396c-3d31-49d9-a20a-d659e204418a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_called</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-34564cef-57bf-4319-8410-73cb35c83953' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-34564cef-57bf-4319-8410-73cb35c83953' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bd151be7-abcb-490e-920b-dd66fe6fe52e' class='xr-var-data-in' type='checkbox'><label for='data-bd151be7-abcb-490e-920b-dd66fe6fe52e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17460,7 +17460,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-945cf7cf-1a7a-49c0-ac6e-4f5966e57f4e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-945cf7cf-1a7a-49c0-ac6e-4f5966e57f4e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7c57a912-f5ec-4714-98a4-c7e289b32f8f' class='xr-var-data-in' type='checkbox'><label for='data-7c57a912-f5ec-4714-98a4-c7e289b32f8f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_call_rate</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-504a14e0-2d6d-46d0-a40d-144b60b19595' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-504a14e0-2d6d-46d0-a40d-144b60b19595' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c4ae5105-f421-45e1-b43c-caefddd0593b' class='xr-var-data-in' type='checkbox'><label for='data-c4ae5105-f421-45e1-b43c-caefddd0593b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17515,7 +17515,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-4b6afba5-b195-4c79-a5c4-7dbe6ddd56f2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4b6afba5-b195-4c79-a5c4-7dbe6ddd56f2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-90926c5c-09c1-49e9-b58e-9d398215385e' class='xr-var-data-in' type='checkbox'><label for='data-90926c5c-09c1-49e9-b58e-9d398215385e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_het</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-d7b586c2-df53-44f7-8940-bcca0c755e79' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d7b586c2-df53-44f7-8940-bcca0c755e79' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-816fd20d-3240-49e3-aefa-70a4b98f5263' class='xr-var-data-in' type='checkbox'><label for='data-816fd20d-3240-49e3-aefa-70a4b98f5263' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17570,7 +17570,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-bafcecc3-66c7-4dd6-8328-5b8c9228152a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-bafcecc3-66c7-4dd6-8328-5b8c9228152a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2c1c7ebd-40bc-41f7-aa25-64fd5014bd3b' class='xr-var-data-in' type='checkbox'><label for='data-2c1c7ebd-40bc-41f7-aa25-64fd5014bd3b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-e9c676a2-3153-441c-9ef0-b13146aa54f9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e9c676a2-3153-441c-9ef0-b13146aa54f9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4cdd192a-c9b4-41da-ae7b-fd0d3f0f1bdc' class='xr-var-data-in' type='checkbox'><label for='data-4cdd192a-c9b4-41da-ae7b-fd0d3f0f1bdc' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17625,7 +17625,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-70d49c35-3bed-4b8a-83e3-9491d8d0580f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-70d49c35-3bed-4b8a-83e3-9491d8d0580f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ac68da5e-4023-491e-a5a5-878031415d0c' class='xr-var-data-in' type='checkbox'><label for='data-ac68da5e-4023-491e-a5a5-878031415d0c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_hom_alt</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-f27783c0-adaa-4dad-b966-295e9f025a57' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f27783c0-adaa-4dad-b966-295e9f025a57' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-177b2b02-9bab-4bb0-953e-217184c60295' class='xr-var-data-in' type='checkbox'><label for='data-177b2b02-9bab-4bb0-953e-217184c60295' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17680,7 +17680,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-80d4e886-9612-4a68-bf3f-f2ee97af47c1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-80d4e886-9612-4a68-bf3f-f2ee97af47c1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a293e24a-bbf3-468d-b6ed-981c31fabb5e' class='xr-var-data-in' type='checkbox'><label for='data-a293e24a-bbf3-468d-b6ed-981c31fabb5e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_n_non_ref</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-0d37f898-f8de-4f7d-83bb-0b9b9925bcc4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0d37f898-f8de-4f7d-83bb-0b9b9925bcc4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6d618f26-0fc4-405f-b261-f77ce617592b' class='xr-var-data-in' type='checkbox'><label for='data-6d618f26-0fc4-405f-b261-f77ce617592b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17735,7 +17735,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-876e9088-2529-4a18-be7b-976ac5c16db5' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-876e9088-2529-4a18-be7b-976ac5c16db5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-42dbed0e-ea9f-45e1-acfe-1a32b0d6afff' class='xr-var-data-in' type='checkbox'><label for='data-42dbed0e-ea9f-45e1-acfe-1a32b0d6afff' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_count</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>uint64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-1f5e4a3e-5028-493c-a811-d4541c94b693' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1f5e4a3e-5028-493c-a811-d4541c94b693' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-247b60e2-5b2c-4a9e-8e03-68c3bd0d39c5' class='xr-var-data-in' type='checkbox'><label for='data-247b60e2-5b2c-4a9e-8e03-68c3bd0d39c5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Variant allele counts. With shape (variants, alleles) and values
 corresponding to the number of non-missing occurrences of each allele.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -17791,7 +17791,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-af2b3d86-824e-4d64-acf6-75688e6b5fb9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-af2b3d86-824e-4d64-acf6-75688e6b5fb9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5198fe4f-0310-4ddf-b9d8-37c9c0d428bd' class='xr-var-data-in' type='checkbox'><label for='data-5198fe4f-0310-4ddf-b9d8-37c9c0d428bd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_total</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-7f9ed6b2-4a7c-411d-992c-76236674c7ea' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7f9ed6b2-4a7c-411d-992c-76236674c7ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-08d3c4ea-ea96-46c5-8566-97f3e2116048' class='xr-var-data-in' type='checkbox'><label for='data-08d3c4ea-ea96-46c5-8566-97f3e2116048' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17846,7 +17846,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-42a0bee7-0db9-4c6b-b350-7104a005bdd3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-42a0bee7-0db9-4c6b-b350-7104a005bdd3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-622cd88b-6d36-48a8-a07f-caf3f89e01c5' class='xr-var-data-in' type='checkbox'><label for='data-622cd88b-6d36-48a8-a07f-caf3f89e01c5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele_frequency</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-3c38db62-0956-45d0-82f4-4d405429688a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3c38db62-0956-45d0-82f4-4d405429688a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-40500feb-359a-4614-a00b-319d559598bd' class='xr-var-data-in' type='checkbox'><label for='data-40500feb-359a-4614-a00b-319d559598bd' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17901,7 +17901,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-6b4b0174-5847-424d-9562-da1619a8d775' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6b4b0174-5847-424d-9562-da1619a8d775' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-22882d61-a3b1-4c9d-a2b0-a3c646c84475' class='xr-var-data-in' type='checkbox'><label for='data-22882d61-a3b1-4c9d-a2b0-a3c646c84475' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_called</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-76ea1e42-072d-4db9-9d27-3eced69dcc04' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-76ea1e42-072d-4db9-9d27-3eced69dcc04' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b8e30306-f4f1-42c5-a5b3-5cbd28dd4d85' class='xr-var-data-in' type='checkbox'><label for='data-b8e30306-f4f1-42c5-a5b3-5cbd28dd4d85' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -17956,7 +17956,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-c364ae72-54f2-4c58-aab4-fe1ff3eb5018' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-c364ae72-54f2-4c58-aab4-fe1ff3eb5018' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c758677f-e020-42a8-8b68-71f99ae16141' class='xr-var-data-in' type='checkbox'><label for='data-c758677f-e020-42a8-8b68-71f99ae16141' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_call_rate</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-cf50cd85-6973-4bc2-bd22-4622df32b993' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-cf50cd85-6973-4bc2-bd22-4622df32b993' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-65c890f6-2a82-4c34-b90a-050e2504824e' class='xr-var-data-in' type='checkbox'><label for='data-65c890f6-2a82-4c34-b90a-050e2504824e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Sample call rate</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18011,7 +18011,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-d8caf861-2b85-4fcf-997f-34ae219ef3da' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d8caf861-2b85-4fcf-997f-34ae219ef3da' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-aeb791d4-7289-4a22-8cdb-71633c073fa2' class='xr-var-data-in' type='checkbox'><label for='data-aeb791d4-7289-4a22-8cdb-71633c073fa2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_het</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-9e98d8ca-a746-4536-bf80-8a0bf0c3fced' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9e98d8ca-a746-4536-bf80-8a0bf0c3fced' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ad1add3f-ed98-4526-a98b-269433e572b2' class='xr-var-data-in' type='checkbox'><label for='data-ad1add3f-ed98-4526-a98b-269433e572b2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18066,7 +18066,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-44bcc349-3dae-4bf2-8565-4af3befd46e9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-44bcc349-3dae-4bf2-8565-4af3befd46e9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-652c59ca-fc5c-4dec-ab6d-f6abde88757e' class='xr-var-data-in' type='checkbox'><label for='data-652c59ca-fc5c-4dec-ab6d-f6abde88757e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-b16dfa03-3232-467c-b31a-107ece84c556' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b16dfa03-3232-467c-b31a-107ece84c556' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-467db307-3772-4b25-b9b5-3b1598d1465d' class='xr-var-data-in' type='checkbox'><label for='data-467db307-3772-4b25-b9b5-3b1598d1465d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18121,7 +18121,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-ee5d9a1c-a440-4901-905f-2a7733dd84e4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ee5d9a1c-a440-4901-905f-2a7733dd84e4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-42ddbf75-e4f7-4513-819e-53a058b7745c' class='xr-var-data-in' type='checkbox'><label for='data-42ddbf75-e4f7-4513-819e-53a058b7745c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_hom_alt</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-6337e052-5f22-4828-8345-80ec03719224' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6337e052-5f22-4828-8345-80ec03719224' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ffa5b75a-6dc6-4007-a961-a2815e5e3b53' class='xr-var-data-in' type='checkbox'><label for='data-ffa5b75a-6dc6-4007-a961-a2815e5e3b53' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18176,7 +18176,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-5f849625-e3fa-4230-8d6a-071fc3023e6d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5f849625-e3fa-4230-8d6a-071fc3023e6d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-85371b3d-1d31-4d5a-abbe-2c9052ad6c01' class='xr-var-data-in' type='checkbox'><label for='data-85371b3d-1d31-4d5a-abbe-2c9052ad6c01' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_n_non_ref</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-978f7ce8-121e-4381-b203-fa98f7603704' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-978f7ce8-121e-4381-b203-fa98f7603704' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-71ea714a-fb49-4103-b931-ee9721805b82' class='xr-var-data-in' type='checkbox'><label for='data-71ea714a-fb49-4103-b931-ee9721805b82' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18231,7 +18231,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-500aed5f-2c9c-4c85-b9f8-38e7d057ccc5' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-500aed5f-2c9c-4c85-b9f8-38e7d057ccc5' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0aac972b-594f-4ebd-bdee-10d1af2d959f' class='xr-var-data-in' type='checkbox'><label for='data-0aac972b-594f-4ebd-bdee-10d1af2d959f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_AD</span></div><div class='xr-var-dims'>(variants, samples, alleles)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-3f1e82eb-d76a-4405-b2ec-7586fcf26a2e' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3f1e82eb-d76a-4405-b2ec-7586fcf26a2e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3a148c3c-523f-4a18-9d36-3dd81eef28b6' class='xr-var-data-in' type='checkbox'><label for='data-3a148c3c-523f-4a18-9d36-3dd81eef28b6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18309,7 +18309,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-32fa2b07-0722-432b-b9d4-a1bc9ea905a0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-32fa2b07-0722-432b-b9d4-a1bc9ea905a0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b2664f3e-682b-4761-b1e6-033f4968da33' class='xr-var-data-in' type='checkbox'><label for='data-b2664f3e-682b-4761-b1e6-033f4968da33' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_DP</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-f2cea24e-ee69-4456-970c-0e5892725f7c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f2cea24e-ee69-4456-970c-0e5892725f7c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-23e3f062-a4da-4e59-b7d1-660361bcb392' class='xr-var-data-in' type='checkbox'><label for='data-23e3f062-a4da-4e59-b7d1-660361bcb392' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18364,7 +18364,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-8d989505-86c2-423f-bd26-3126f1b03a44' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8d989505-86c2-423f-bd26-3126f1b03a44' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-180a86a4-3188-41db-9ba5-f3e68a7ffa94' class='xr-var-data-in' type='checkbox'><label for='data-180a86a4-3188-41db-9ba5-f3e68a7ffa94' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_GQ</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-ba9cab22-9877-4924-9d20-d9e69fe51ee4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ba9cab22-9877-4924-9d20-d9e69fe51ee4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7bf2e64a-e6f1-4455-b70a-6c6741d4dd6e' class='xr-var-data-in' type='checkbox'><label for='data-7bf2e64a-e6f1-4455-b70a-6c6741d4dd6e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18419,7 +18419,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-97acfc70-3ff4-4c7a-9c87-d8cf98e58cdf' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-97acfc70-3ff4-4c7a-9c87-d8cf98e58cdf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5fe0621f-71f1-4fdb-832f-64925ba14575' class='xr-var-data-in' type='checkbox'><label for='data-5fe0621f-71f1-4fdb-832f-64925ba14575' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-50dfb74e-88b3-4482-9465-2d045f2a15db' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-50dfb74e-88b3-4482-9465-2d045f2a15db' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e4c64f74-2d81-4331-b8d3-f82233bad4f3' class='xr-var-data-in' type='checkbox'><label for='data-e4c64f74-2d81-4331-b8d3-f82233bad4f3' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Call genotype. Encoded as allele values (0 for the reference, 1 for
 the first allele, 2 for the second allele), -1 to indicate a
 missing value, or -2 to indicate a non allele in mixed ploidy datasets.</dd><dt><span>mixed_ploidy :</span></dt><dd>False</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -18499,7 +18499,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-787dcc46-20f2-465b-b086-1004bf93c88e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-787dcc46-20f2-465b-b086-1004bf93c88e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-89cfc2b3-a734-4a56-9057-5ec37f96372c' class='xr-var-data-in' type='checkbox'><label for='data-89cfc2b3-a734-4a56-9057-5ec37f96372c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_mask</span></div><div class='xr-var-dims'>(variants, samples, ploidy)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250, 2), meta=np.ndarray&gt;</div><input id='attrs-0a01b51a-12d1-47b3-819e-6a4daca744d8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0a01b51a-12d1-47b3-819e-6a4daca744d8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-07bc4487-b784-4559-bbca-0e1cacefed07' class='xr-var-data-in' type='checkbox'><label for='data-07bc4487-b784-4559-bbca-0e1cacefed07' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating which values are missing.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18577,7 +18577,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-ba476a7a-7c98-4095-9412-d42ddd5dee1e' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ba476a7a-7c98-4095-9412-d42ddd5dee1e' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dfdaef71-7b6d-4d85-a3b5-fb039d322a10' class='xr-var-data-in' type='checkbox'><label for='data-dfdaef71-7b6d-4d85-a3b5-fb039d322a10' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_genotype_phased</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-8aee9ae8-70df-4545-bca8-a833f86e86ea' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-8aee9ae8-70df-4545-bca8-a833f86e86ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9d24230e-3dde-4ffd-b474-4cbd4790a20d' class='xr-var-data-in' type='checkbox'><label for='data-9d24230e-3dde-4ffd-b474-4cbd4790a20d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>A flag for each call indicating if it is phased or not. If omitted
 all calls are unphased.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
@@ -18633,7 +18633,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-e609997c-e59b-4326-93f8-3f75cbb9d2bb' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e609997c-e59b-4326-93f8-3f75cbb9d2bb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6dc97ffd-53d2-4a68-94fd-a3c7d47047c5' class='xr-var-data-in' type='checkbox'><label for='data-6dc97ffd-53d2-4a68-94fd-a3c7d47047c5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_id</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-1dfb2777-28d1-4bc7-8d49-3a519762ceec' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-1dfb2777-28d1-4bc7-8d49-3a519762ceec' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1a5d747c-e664-4a6c-b320-f465b3b498d2' class='xr-var-data-in' type='checkbox'><label for='data-1a5d747c-e664-4a6c-b320-f465b3b498d2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18688,7 +18688,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-38080cf1-eb84-4692-a48c-000799ebded2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-38080cf1-eb84-4692-a48c-000799ebded2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-60909806-72b2-4dd8-8258-aafa084fc046' class='xr-var-data-in' type='checkbox'><label for='data-60909806-72b2-4dd8-8258-aafa084fc046' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>contig_length</span></div><div class='xr-var-dims'>(contigs)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(84,), meta=np.ndarray&gt;</div><input id='attrs-c8c00bdf-d2dc-4e29-8b5d-76e9560ed139' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c8c00bdf-d2dc-4e29-8b5d-76e9560ed139' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f528cb87-beba-4a11-8738-29a5df7d40ce' class='xr-var-data-in' type='checkbox'><label for='data-f528cb87-beba-4a11-8738-29a5df7d40ce' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18743,7 +18743,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-f27d333a-c27e-43b0-a52b-d568ebd2f154' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-f27d333a-c27e-43b0-a52b-d568ebd2f154' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-52abeacd-1f4e-4b1c-9ce8-943691a8cb12' class='xr-var-data-in' type='checkbox'><label for='data-52abeacd-1f4e-4b1c-9ce8-943691a8cb12' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>filter_id</span></div><div class='xr-var-dims'>(filters)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(1,), meta=np.ndarray&gt;</div><input id='attrs-7a938f25-a1bb-4302-aaf5-af397d6fdef4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7a938f25-a1bb-4302-aaf5-af397d6fdef4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-51bb23ab-5771-4550-a8e5-2c926c750ba6' class='xr-var-data-in' type='checkbox'><label for='data-51bb23ab-5771-4550-a8e5-2c926c750ba6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18798,7 +18798,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-e6c43611-98ec-46d8-8cc7-177c038cb5dd' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e6c43611-98ec-46d8-8cc7-177c038cb5dd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-70682940-1538-4d61-a539-20feaefa39b0' class='xr-var-data-in' type='checkbox'><label for='data-70682940-1538-4d61-a539-20feaefa39b0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_allele</span></div><div class='xr-var-dims'>(variants, alleles)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 2), meta=np.ndarray&gt;</div><input id='attrs-ffc8bb28-49b1-45ae-9509-fb515408e71d' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-ffc8bb28-49b1-45ae-9509-fb515408e71d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b6a667db-9e0d-4439-9a9b-78e0ab89fee2' class='xr-var-data-in' type='checkbox'><label for='data-b6a667db-9e0d-4439-9a9b-78e0ab89fee2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The possible alleles for the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18853,7 +18853,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-e1701809-a7cc-4c08-9a8e-a073aee900e7' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-e1701809-a7cc-4c08-9a8e-a073aee900e7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ba09932f-af8b-4ef6-946a-e72381a4d932' class='xr-var-data-in' type='checkbox'><label for='data-ba09932f-af8b-4ef6-946a-e72381a4d932' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int8</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-a319e5a3-09de-4ca9-adde-3544c5616bc2' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a319e5a3-09de-4ca9-adde-3544c5616bc2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6651a16f-4714-444c-aeb6-e7dfabf2c312' class='xr-var-data-in' type='checkbox'><label for='data-6651a16f-4714-444c-aeb6-e7dfabf2c312' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
@@ -18910,7 +18910,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 1), meta=np.ndarray&gt;</div><input id='attrs-263c68d0-7054-4737-b6d8-429d01d1c6fb' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-263c68d0-7054-4737-b6d8-429d01d1c6fb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f8eb10c5-aff9-4dd7-b91b-e28365db8046' class='xr-var-data-in' type='checkbox'><label for='data-f8eb10c5-aff9-4dd7-b91b-e28365db8046' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_filter</span></div><div class='xr-var-dims'>(variants, filters)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 1), meta=np.ndarray&gt;</div><input id='attrs-8191807f-d67f-41ef-af9a-94a73c2f6de0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-8191807f-d67f-41ef-af9a-94a73c2f6de0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2f4d557a-12cf-4289-9f66-0e87563017e1' class='xr-var-data-in' type='checkbox'><label for='data-2f4d557a-12cf-4289-9f66-0e87563017e1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -18965,7 +18965,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-fdb77ee7-5647-45b7-a0db-c9ee51510ab8' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-fdb77ee7-5647-45b7-a0db-c9ee51510ab8' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ac30add0-f64e-4dcb-82a2-ecb4fed6e75c' class='xr-var-data-in' type='checkbox'><label for='data-ac30add0-f64e-4dcb-82a2-ecb4fed6e75c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-0678831f-859a-47bf-b737-4580410f8795' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-0678831f-859a-47bf-b737-4580410f8795' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5e652482-a371-4b8b-afdf-00e9f5e7294d' class='xr-var-data-in' type='checkbox'><label for='data-5e652482-a371-4b8b-afdf-00e9f5e7294d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The unique identifier of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19020,7 +19020,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-1ced4d0a-d2fa-4d3f-b4f3-8df1ea5862a9' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-1ced4d0a-d2fa-4d3f-b4f3-8df1ea5862a9' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1c5f515a-402f-4f54-8a1c-bdae2fef5a4f' class='xr-var-data-in' type='checkbox'><label for='data-1c5f515a-402f-4f54-8a1c-bdae2fef5a4f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_id_mask</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-c3fbfc3c-9fff-4ad0-a8bb-356252e1f6e7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c3fbfc3c-9fff-4ad0-a8bb-356252e1f6e7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ca74364b-15df-4e53-bd70-74d4710fee85' class='xr-var-data-in' type='checkbox'><label for='data-ca74364b-15df-4e53-bd70-74d4710fee85' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19075,7 +19075,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-3049ec10-404c-4288-9108-7fba017dad04' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3049ec10-404c-4288-9108-7fba017dad04' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fea406f8-5cbd-4df0-9d59-4b7ab1caaa80' class='xr-var-data-in' type='checkbox'><label for='data-fea406f8-5cbd-4df0-9d59-4b7ab1caaa80' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_position</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>int32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-3423c44e-c756-4b2d-8d88-1dcca7f88fdf' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-3423c44e-c756-4b2d-8d88-1dcca7f88fdf' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-88628a32-48e3-4424-88f6-1bd84eb5659d' class='xr-var-data-in' type='checkbox'><label for='data-88628a32-48e3-4424-88f6-1bd84eb5659d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>The reference position of the variant.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19130,7 +19130,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-5af159a7-a86f-4506-87b4-29ce009e1a98' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5af159a7-a86f-4506-87b4-29ce009e1a98' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-162fb9d6-e0d6-4f37-b226-5ac7c7f8791a' class='xr-var-data-in' type='checkbox'><label for='data-162fb9d6-e0d6-4f37-b226-5ac7c7f8791a' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_quality</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>float32</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-b8faa21a-6748-430c-8c77-f2faed93d2ff' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b8faa21a-6748-430c-8c77-f2faed93d2ff' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f68916ee-b360-42be-ab5f-690b9b0551de' class='xr-var-data-in' type='checkbox'><label for='data-f68916ee-b360-42be-ab5f-690b9b0551de' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19185,7 +19185,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-a7341249-413b-4779-a791-1bf045973c5f' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-a7341249-413b-4779-a791-1bf045973c5f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d9d9f4ce-5505-4c65-91c5-9ffdcd392793' class='xr-var-data-in' type='checkbox'><label for='data-d9d9f4ce-5505-4c65-91c5-9ffdcd392793' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>variant_contig_name</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>&lt;U10</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491,), meta=np.ndarray&gt;</div><input id='attrs-d1ec3a09-9998-4147-8018-435650cad762' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-d1ec3a09-9998-4147-8018-435650cad762' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5bdd794a-3b9f-413d-8b73-a563f31b6014' class='xr-var-data-in' type='checkbox'><label for='data-5bdd794a-3b9f-413d-8b73-a563f31b6014' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Contig identifiers.</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19240,7 +19240,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-0e26488a-7496-4752-ab87-7e9cc998bd5b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0e26488a-7496-4752-ab87-7e9cc998bd5b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-09c7fcce-be62-4e54-bc2a-f9e04268a065' class='xr-var-data-in' type='checkbox'><label for='data-09c7fcce-be62-4e54-bc2a-f9e04268a065' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>Population</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;GBR&#x27; &#x27;GBR&#x27; &#x27;GBR&#x27; ... &#x27;GIH&#x27; &#x27;GIH&#x27;</div><input id='attrs-5851142c-afad-41c6-8943-86dada14f4c7' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5851142c-afad-41c6-8943-86dada14f4c7' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-fe630a1c-0f2a-48c8-85e6-a129c5a0cd02' class='xr-var-data-in' type='checkbox'><label for='data-fe630a1c-0f2a-48c8-85e6-a129c5a0cd02' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;GBR&#x27;, &#x27;FIN&#x27;, &#x27;FIN&#x27;,
        &#x27;FIN&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;,
        &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;CHS&#x27;, &#x27;PUR&#x27;, &#x27;CDX&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;,
        &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;PUR&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;CLM&#x27;, &#x27;GBR&#x27;, &#x27;CLM&#x27;,
@@ -19267,7 +19267,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
        &#x27;LWK&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;MXL&#x27;, &#x27;MXL&#x27;,
        &#x27;MXL&#x27;, &#x27;ASW&#x27;, &#x27;ASW&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;,
        &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;TSI&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;,
-       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-a6e168c0-634c-4bbb-848c-5b851a96f0ac' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a6e168c0-634c-4bbb-848c-5b851a96f0ac' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-15289b96-210f-4e92-a61f-2b9781843008' class='xr-var-data-in' type='checkbox'><label for='data-15289b96-210f-4e92-a61f-2b9781843008' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
+       &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;, &#x27;GIH&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>SuperPopulation</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;EUR&#x27; &#x27;EUR&#x27; &#x27;EUR&#x27; ... &#x27;SAS&#x27; &#x27;SAS&#x27;</div><input id='attrs-d5c67362-2d80-45f0-9d81-33a5b60180be' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-d5c67362-2d80-45f0-9d81-33a5b60180be' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9c23f637-b7a4-47de-8d17-4a6f63f877a6' class='xr-var-data-in' type='checkbox'><label for='data-9c23f637-b7a4-47de-8d17-4a6f63f877a6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;,
        &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;EAS&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;EUR&#x27;, &#x27;AMR&#x27;,
@@ -19294,7 +19294,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
        &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AMR&#x27;, &#x27;AMR&#x27;,
        &#x27;AMR&#x27;, &#x27;AFR&#x27;, &#x27;AFR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;,
        &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;EUR&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;,
-       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-2a7f973e-60fb-446c-be9b-f67adabf3570' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2a7f973e-60fb-446c-be9b-f67adabf3570' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d8872480-639b-456e-8d2f-151451eeb846' class='xr-var-data-in' type='checkbox'><label for='data-d8872480-639b-456e-8d2f-151451eeb846' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
+       &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;, &#x27;SAS&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>isFemale</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False True False ... False True</div><input id='attrs-9041f246-6e3e-4fe5-8422-2401a4106bc2' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-9041f246-6e3e-4fe5-8422-2401a4106bc2' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-62a10f6d-110e-4efc-989c-de7b6757823f' class='xr-var-data-in' type='checkbox'><label for='data-62a10f6d-110e-4efc-989c-de7b6757823f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False,  True, False,  True, False, False,  True, False,  True,
        False, False,  True, False,  True, False, False, False,  True,
         True,  True, False,  True,  True, False,  True,  True, False,
        False,  True, False,  True, False,  True,  True, False,  True,
@@ -19321,7 +19321,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
         True, False,  True, False,  True, False,  True, False, False,
         True, False, False,  True, False,  True,  True,  True, False,
         True, False,  True, False, False,  True,  True,  True,  True,
-        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-89b4bb1b-e038-4b87-a6e4-6754d418e685' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-89b4bb1b-e038-4b87-a6e4-6754d418e685' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6066d9ba-0130-47cd-abd7-06f52c2b2f9f' class='xr-var-data-in' type='checkbox'><label for='data-6066d9ba-0130-47cd-abd7-06f52c2b2f9f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
+        True, False, False, False, False, False,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>PurpleHair</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>bool</div><div class='xr-var-preview xr-preview'>False False False ... True True</div><input id='attrs-7e0249d2-8402-44cc-bd73-9fdbf59f4272' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7e0249d2-8402-44cc-bd73-9fdbf59f4272' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-93a9ffed-bb52-44b6-aad2-f84d8ee96362' class='xr-var-data-in' type='checkbox'><label for='data-93a9ffed-bb52-44b6-aad2-f84d8ee96362' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([False, False, False, False, False,  True, False, False,  True,
         True, False, False,  True,  True,  True,  True,  True,  True,
         True, False,  True,  True, False, False, False, False, False,
         True, False,  True,  True,  True, False,  True, False,  True,
@@ -19348,7 +19348,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
        False,  True,  True, False, False, False, False,  True, False,
         True, False,  True,  True, False, False, False, False,  True,
         True,  True,  True,  True,  True, False, False,  True, False,
-       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-7f489aac-1835-4ee4-b96f-63a520d65f5d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7f489aac-1835-4ee4-b96f-63a520d65f5d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-acc7ea63-e223-4068-a1d7-123f7e5b74d8' class='xr-var-data-in' type='checkbox'><label for='data-acc7ea63-e223-4068-a1d7-123f7e5b74d8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
+       False,  True,  True,  True, False,  True,  True])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>CaffeineConsumption</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>4 4 4 3 6 2 2 5 ... 5 6 4 6 4 6 5 5</div><input id='attrs-2cabad2d-e316-433f-9537-3e991903bf35' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2cabad2d-e316-433f-9537-3e991903bf35' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-5c54852c-6fd1-456d-9c00-abf969abda14' class='xr-var-data-in' type='checkbox'><label for='data-5c54852c-6fd1-456d-9c00-abf969abda14' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([4, 4, 4, 3, 6, 2, 2, 5, 5, 4, 6, 5, 7, 5, 7, 1, 5, 5, 4, 4, 5, 5,
        5, 6, 4, 4, 6, 3, 3, 5, 4, 4, 5, 5, 4, 6, 5, 4, 4, 5, 6, 3, 7, 5,
        5, 6, 3, 2, 5, 5, 4, 6, 5, 6, 4, 6, 7, 6, 7, 3, 5, 6, 5, 6, 4, 5,
        4, 4, 5, 8, 3, 4, 4, 7, 5, 2, 6, 7, 6, 5, 3, 4, 5, 5, 5, 5, 6, 4,
@@ -19359,7 +19359,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
        7, 5, 6, 6, 4, 4, 5, 3, 5, 4, 3, 8, 4, 6, 8, 3, 4, 2, 5, 6, 6, 4,
        3, 5, 7, 4, 5, 5, 6, 3, 2, 4, 5, 6, 7, 2, 4, 2, 1, 5, 3, 4, 9, 6,
        4, 3, 4, 4, 6, 7, 6, 3, 4, 3, 6, 6, 3, 4, 4, 4, 6, 7, 4, 5, 4, 5,
-       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-b54ff950-463e-4379-a8d7-ac46404b84ba' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-b54ff950-463e-4379-a8d7-ac46404b84ba' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3a3d79cc-024d-4259-9a2d-b9e250b95873' class='xr-var-data-in' type='checkbox'><label for='data-3a3d79cc-024d-4259-9a2d-b9e250b95873' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
+       5, 6, 4, 6, 4, 6, 5, 5])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>sample_dp_mean</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(250,), meta=np.ndarray&gt;</div><input id='attrs-9e5da6af-fdd3-4e9a-9ae1-2cda450f05cb' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-9e5da6af-fdd3-4e9a-9ae1-2cda450f05cb' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-08d2518e-3199-401b-b45e-e312972dbec4' class='xr-var-data-in' type='checkbox'><label for='data-08d2518e-3199-401b-b45e-e312972dbec4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>long_name :</span></dt><dd>Mean Sample DP</dd></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19414,7 +19414,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-4aea7140-f014-45fd-9807-09ca56b3323a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-4aea7140-f014-45fd-9807-09ca56b3323a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-32654e54-6558-4fb6-883c-2e459ebdf1d1' class='xr-var-data-in' type='checkbox'><label for='data-32654e54-6558-4fb6-883c-2e459ebdf1d1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
+</table></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>int64</div><div class='xr-var-preview xr-preview'>dask.array&lt;chunksize=(3491, 250), meta=np.ndarray&gt;</div><input id='attrs-22a51399-da01-40dd-8ce4-a138e16eb056' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-22a51399-da01-40dd-8ce4-a138e16eb056' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-9ff6bfd3-6e96-4175-801c-e35aac9636eb' class='xr-var-data-in' type='checkbox'><label for='data-9ff6bfd3-6e96-4175-801c-e35aac9636eb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -19469,7 +19469,7 @@ <h2>Confounded!<a class="headerlink" href="#confounded" title="Permalink to this
 </svg>
         </td>
     </tr>
-</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-20fcde6c-06a7-4839-bb83-8d8936bf42d1' class='xr-section-summary-in' type='checkbox'  ><label for='section-20fcde6c-06a7-4839-bb83-8d8936bf42d1' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-12c977ad-784e-4786-81c1-af0e504afa40' class='xr-index-data-in' type='checkbox'/><label for='index-12c977ad-784e-4786-81c1-af0e504afa40' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-ee3f0de3-5822-4c98-9b4b-a6ec73dacc0c' class='xr-section-summary-in' type='checkbox'  ><label for='section-ee3f0de3-5822-4c98-9b4b-a6ec73dacc0c' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
+</table></div></li></ul></div></li><li class='xr-section-item'><input id='section-6742fddb-f292-4034-b0ad-4a43917c513e' class='xr-section-summary-in' type='checkbox'  ><label for='section-6742fddb-f292-4034-b0ad-4a43917c513e' class='xr-section-summary' >Indexes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>genotypes</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-98de3b2d-e218-42f5-adde-0ca426632e24' class='xr-index-data-in' type='checkbox'/><label for='index-98de3b2d-e218-42f5-adde-0ca426632e24' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;0/0&#x27;, &#x27;0/1&#x27;, &#x27;1/1&#x27;], dtype=&#x27;object&#x27;, name=&#x27;genotypes&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-139c875a-5c10-4f24-89a9-447a496273b4' class='xr-section-summary-in' type='checkbox'  ><label for='section-139c875a-5c10-4f24-89a9-447a496273b4' class='xr-section-summary' >Attributes: <span>(7)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>contig_lengths :</span></dt><dd>[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496]</dd><dt><span>contigs :</span></dt><dd>[&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;, &#x27;11&#x27;, &#x27;12&#x27;, &#x27;13&#x27;, &#x27;14&#x27;, &#x27;15&#x27;, &#x27;16&#x27;, &#x27;17&#x27;, &#x27;18&#x27;, &#x27;19&#x27;, &#x27;20&#x27;, &#x27;21&#x27;, &#x27;22&#x27;, &#x27;X&#x27;, &#x27;Y&#x27;, &#x27;MT&#x27;, &#x27;GL000207.1&#x27;, &#x27;GL000226.1&#x27;, &#x27;GL000229.1&#x27;, &#x27;GL000231.1&#x27;, &#x27;GL000210.1&#x27;, &#x27;GL000239.1&#x27;, &#x27;GL000235.1&#x27;, &#x27;GL000201.1&#x27;, &#x27;GL000247.1&#x27;, &#x27;GL000245.1&#x27;, &#x27;GL000197.1&#x27;, &#x27;GL000203.1&#x27;, &#x27;GL000246.1&#x27;, &#x27;GL000249.1&#x27;, &#x27;GL000196.1&#x27;, &#x27;GL000248.1&#x27;, &#x27;GL000244.1&#x27;, &#x27;GL000238.1&#x27;, &#x27;GL000202.1&#x27;, &#x27;GL000234.1&#x27;, &#x27;GL000232.1&#x27;, &#x27;GL000206.1&#x27;, &#x27;GL000240.1&#x27;, &#x27;GL000236.1&#x27;, &#x27;GL000241.1&#x27;, &#x27;GL000243.1&#x27;, &#x27;GL000242.1&#x27;, &#x27;GL000230.1&#x27;, &#x27;GL000237.1&#x27;, &#x27;GL000233.1&#x27;, &#x27;GL000204.1&#x27;, &#x27;GL000198.1&#x27;, &#x27;GL000208.1&#x27;, &#x27;GL000191.1&#x27;, &#x27;GL000227.1&#x27;, &#x27;GL000228.1&#x27;, &#x27;GL000214.1&#x27;, &#x27;GL000221.1&#x27;, &#x27;GL000209.1&#x27;, &#x27;GL000218.1&#x27;, &#x27;GL000220.1&#x27;, &#x27;GL000213.1&#x27;, &#x27;GL000211.1&#x27;, &#x27;GL000199.1&#x27;, &#x27;GL000217.1&#x27;, &#x27;GL000216.1&#x27;, &#x27;GL000215.1&#x27;, &#x27;GL000205.1&#x27;, &#x27;GL000219.1&#x27;, &#x27;GL000224.1&#x27;, &#x27;GL000223.1&#x27;, &#x27;GL000195.1&#x27;, &#x27;GL000212.1&#x27;, &#x27;GL000222.1&#x27;, &#x27;GL000200.1&#x27;, &#x27;GL000193.1&#x27;, &#x27;GL000194.1&#x27;, &#x27;GL000225.1&#x27;, &#x27;GL000192.1&#x27;]</dd><dt><span>filters :</span></dt><dd>[&#x27;PASS&#x27;]</dd><dt><span>max_alt_alleles_seen :</span></dt><dd>1</dd><dt><span>source :</span></dt><dd>sgkit-unknown</dd><dt><span>vcf_header :</span></dt><dd>##fileformat=VCFv4.2
 ##FILTER=&lt;ID=PASS,Description=&quot;All filters passed&quot;&gt;
 ##hailversion=0.2-29fbaeaf265e
 ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;&quot;&gt;
diff --git a/latest/examples/relatedness_tutorial.html b/latest/examples/relatedness_tutorial.html
index 916ecd4ed..b2e61ef47 100644
--- a/latest/examples/relatedness_tutorial.html
+++ b/latest/examples/relatedness_tutorial.html
@@ -1153,17 +1153,17 @@ <h2>Reading pedigree data<a class="headerlink" href="#reading-pedigree-data" tit
        [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)
 Coordinates:
   * samples  (samples) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
-  * parents  (parents) object 16B &#x27;SIRE&#x27; &#x27;DAM&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-53bda7c9-2bcf-4fca-9cd1-456dff9538c8' class='xr-array-in' type='checkbox' checked><label for='section-53bda7c9-2bcf-4fca-9cd1-456dff9538c8' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>&#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;4279&#x27; &#x27;6465&#x27; &#x27;6466&#x27; &#x27;1129&#x27; &#x27;5129&#x27; &#x27;6472&#x27;</span></div><div class='xr-array-data'><pre>array([[&#x27;.&#x27;, &#x27;.&#x27;],
+  * parents  (parents) object 16B &#x27;SIRE&#x27; &#x27;DAM&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-3002cda2-d0f7-4011-b753-3d5b6c319e3e' class='xr-array-in' type='checkbox' checked><label for='section-3002cda2-d0f7-4011-b753-3d5b6c319e3e' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>&#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;4279&#x27; &#x27;6465&#x27; &#x27;6466&#x27; &#x27;1129&#x27; &#x27;5129&#x27; &#x27;6472&#x27;</span></div><div class='xr-array-data'><pre>array([[&#x27;.&#x27;, &#x27;.&#x27;],
        [&#x27;.&#x27;, &#x27;.&#x27;],
        [&#x27;.&#x27;, &#x27;.&#x27;],
        ...,
        [&#x27;4279&#x27;, &#x27;6465&#x27;],
        [&#x27;6466&#x27;, &#x27;1129&#x27;],
-       [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)</pre></div></div></li><li class='xr-section-item'><input id='section-67dedb19-d635-4405-81c1-89304ddf3dea' class='xr-section-summary-in' type='checkbox'  checked><label for='section-67dedb19-d635-4405-81c1-89304ddf3dea' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-298a53fa-7865-4e3e-afbd-58e2fe150e7a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-298a53fa-7865-4e3e-afbd-58e2fe150e7a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a0ef560c-419f-48d4-ae3a-9abe5269ad63' class='xr-var-data-in' type='checkbox'><label for='data-a0ef560c-419f-48d4-ae3a-9abe5269ad63' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-19394644-b04b-46c6-91a1-759aad5a09c4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-19394644-b04b-46c6-91a1-759aad5a09c4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-dff2f41a-a2ad-432f-9fb8-4e48d3d2a2d5' class='xr-var-data-in' type='checkbox'><label for='data-dff2f41a-a2ad-432f-9fb8-4e48d3d2a2d5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-10724527-67ee-4470-9396-215b920889df' class='xr-section-summary-in' type='checkbox'  ><label for='section-10724527-67ee-4470-9396-215b920889df' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-ad808f9d-902b-407a-aaeb-fd4cbe5cbff4' class='xr-index-data-in' type='checkbox'/><label for='index-ad808f9d-902b-407a-aaeb-fd4cbe5cbff4' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+       [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)</pre></div></div></li><li class='xr-section-item'><input id='section-d0940488-0f72-4242-8b57-e34c20f69a71' class='xr-section-summary-in' type='checkbox'  checked><label for='section-d0940488-0f72-4242-8b57-e34c20f69a71' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-fd1852b9-9239-4841-9fb3-15539d9e4fb4' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-fd1852b9-9239-4841-9fb3-15539d9e4fb4' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-980165f9-40df-4070-bcb8-f7c573932668' class='xr-var-data-in' type='checkbox'><label for='data-980165f9-40df-4070-bcb8-f7c573932668' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-70a46af4-af88-4025-961e-90d66f7efe14' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-70a46af4-af88-4025-961e-90d66f7efe14' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-3c3e4228-e4f8-4da8-89c8-bd8f4b67955d' class='xr-var-data-in' type='checkbox'><label for='data-3c3e4228-e4f8-4da8-89c8-bd8f4b67955d' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-29b237c2-296d-4054-aa47-42653c8cf7c0' class='xr-section-summary-in' type='checkbox'  ><label for='section-29b237c2-296d-4054-aa47-42653c8cf7c0' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-2a4e7bb3-8f6b-4813-a190-002b4234eb10' class='xr-index-data-in' type='checkbox'/><label for='index-2a4e7bb3-8f6b-4813-a190-002b4234eb10' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-ed982677-a9af-4a99-810b-cd8e8257f62e' class='xr-index-data-in' type='checkbox'/><label for='index-ed982677-a9af-4a99-810b-cd8e8257f62e' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-0089ec5d-106c-4e40-a62e-c56ee5840f83' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-0089ec5d-106c-4e40-a62e-c56ee5840f83' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-9885df45-8e10-4776-b0f2-6f0f1a851443' class='xr-index-data-in' type='checkbox'/><label for='index-9885df45-8e10-4776-b0f2-6f0f1a851443' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-bc645df2-d08a-4fb0-81d7-4155ed0781b0' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-bc645df2-d08a-4fb0-81d7-4155ed0781b0' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
 </div>
 <p>Note that the index column of the pedigree dataframe (containing the sample IDs) has been translated to <em>coordinates</em> for the “samples” dimension of the data array.
 Likewise, the column names have been used as coordinates of the “parents” dimension.</p>
@@ -1552,17 +1552,17 @@ <h2>Reading pedigree data<a class="headerlink" href="#reading-pedigree-data" tit
   * parents    (parents) object 16B &#x27;SIRE&#x27; &#x27;DAM&#x27;
 Data variables:
     sample_id  (samples) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
-    parent_id  (samples, parents) object 104kB &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;5129&#x27; &#x27;6472&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-25a8484f-e5a3-48a9-b7e9-197eca9221b2' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-25a8484f-e5a3-48a9-b7e9-197eca9221b2' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-1dcc5cf1-a446-4bb5-9375-de044aa9f91e' class='xr-section-summary-in' type='checkbox'  checked><label for='section-1dcc5cf1-a446-4bb5-9375-de044aa9f91e' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-6f3a4a23-f901-4dc1-b113-1122976d4c96' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6f3a4a23-f901-4dc1-b113-1122976d4c96' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-041b57db-fc17-4f00-b305-5635417248e0' class='xr-var-data-in' type='checkbox'><label for='data-041b57db-fc17-4f00-b305-5635417248e0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-ac58f143-5ca5-42d5-811a-e48668c829ea' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ac58f143-5ca5-42d5-811a-e48668c829ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-33d87267-b4f8-4378-91ac-da44206612a6' class='xr-var-data-in' type='checkbox'><label for='data-33d87267-b4f8-4378-91ac-da44206612a6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b9c13f14-71f5-4f4e-a5ac-8961b0abe370' class='xr-section-summary-in' type='checkbox'  checked><label for='section-b9c13f14-71f5-4f4e-a5ac-8961b0abe370' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-a435f816-9c97-471c-8098-8f6f038576ff' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a435f816-9c97-471c-8098-8f6f038576ff' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-6fcf5661-20aa-4170-a8c9-6669b0cd642e' class='xr-var-data-in' type='checkbox'><label for='data-6fcf5661-20aa-4170-a8c9-6669b0cd642e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>parent_id</span></div><div class='xr-var-dims'>(samples, parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;5129&#x27; &#x27;6472&#x27;</div><input id='attrs-7054c930-b79d-4b9a-8b60-27201e13d707' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7054c930-b79d-4b9a-8b60-27201e13d707' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a80722dc-861d-451d-b698-1e6535ac846b' class='xr-var-data-in' type='checkbox'><label for='data-a80722dc-861d-451d-b698-1e6535ac846b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([[&#x27;.&#x27;, &#x27;.&#x27;],
+    parent_id  (samples, parents) object 104kB &#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;5129&#x27; &#x27;6472&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-02164ad9-0ad7-4e07-99cb-f7fc37ae31b6' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-02164ad9-0ad7-4e07-99cb-f7fc37ae31b6' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-678b5710-3a0f-4916-b767-2be3d86944bd' class='xr-section-summary-in' type='checkbox'  checked><label for='section-678b5710-3a0f-4916-b767-2be3d86944bd' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-6a540558-c410-4022-aea6-dfa3538c7b9f' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6a540558-c410-4022-aea6-dfa3538c7b9f' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b227bb2c-f17b-4312-a547-56818bb8d6a7' class='xr-var-data-in' type='checkbox'><label for='data-b227bb2c-f17b-4312-a547-56818bb8d6a7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-dabac15d-6c97-4981-9f20-c064c3a6d5ea' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dabac15d-6c97-4981-9f20-c064c3a6d5ea' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-cfef41e1-5e49-44d8-aedd-f6e9c2fb408f' class='xr-var-data-in' type='checkbox'><label for='data-cfef41e1-5e49-44d8-aedd-f6e9c2fb408f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-7b14ef96-9ff8-4528-94e7-8910a6fc4c57' class='xr-section-summary-in' type='checkbox'  checked><label for='section-7b14ef96-9ff8-4528-94e7-8910a6fc4c57' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-30268c85-d67a-4e8b-97db-3e769c0bec9b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-30268c85-d67a-4e8b-97db-3e769c0bec9b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-35302813-e1f5-4fa9-b32f-b455a3599fe8' class='xr-var-data-in' type='checkbox'><label for='data-35302813-e1f5-4fa9-b32f-b455a3599fe8' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>parent_id</span></div><div class='xr-var-dims'>(samples, parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;.&#x27; &#x27;.&#x27; &#x27;.&#x27; ... &#x27;5129&#x27; &#x27;6472&#x27;</div><input id='attrs-057199ef-8563-4136-a085-3de3b2150bfd' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-057199ef-8563-4136-a085-3de3b2150bfd' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e7587e04-42f1-4293-bd34-609af24183a5' class='xr-var-data-in' type='checkbox'><label for='data-e7587e04-42f1-4293-bd34-609af24183a5' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([[&#x27;.&#x27;, &#x27;.&#x27;],
        [&#x27;.&#x27;, &#x27;.&#x27;],
        [&#x27;.&#x27;, &#x27;.&#x27;],
        ...,
        [&#x27;4279&#x27;, &#x27;6465&#x27;],
        [&#x27;6466&#x27;, &#x27;1129&#x27;],
-       [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-efd57c1c-9337-4c94-ba88-9489556a8012' class='xr-section-summary-in' type='checkbox'  ><label for='section-efd57c1c-9337-4c94-ba88-9489556a8012' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-a57f634e-4910-4c23-b54a-f7e163a846eb' class='xr-index-data-in' type='checkbox'/><label for='index-a57f634e-4910-4c23-b54a-f7e163a846eb' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+       [&#x27;5129&#x27;, &#x27;6472&#x27;]], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-e41ab16b-6052-4ed0-a55b-04265781563b' class='xr-section-summary-in' type='checkbox'  ><label for='section-e41ab16b-6052-4ed0-a55b-04265781563b' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-0b85b09b-0806-41c3-9964-28fb34b5b348' class='xr-index-data-in' type='checkbox'/><label for='index-0b85b09b-0806-41c3-9964-28fb34b5b348' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-776d030f-3c29-4862-8162-b89fba5adcac' class='xr-index-data-in' type='checkbox'/><label for='index-776d030f-3c29-4862-8162-b89fba5adcac' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b1161fc5-1ce2-462c-864b-0112694d448c' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-b1161fc5-1ce2-462c-864b-0112694d448c' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-e3af8026-e069-42b8-9729-8c2184d24465' class='xr-index-data-in' type='checkbox'/><label for='index-e3af8026-e069-42b8-9729-8c2184d24465' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-330836ab-4887-4a41-b374-6b8058cac173' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-330836ab-4887-4a41-b374-6b8058cac173' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
 </div>
 </section>
 <section id="working-with-pedigree-data">
@@ -1957,17 +1957,17 @@ <h2>Working with pedigree data<a class="headerlink" href="#working-with-pedigree
   * samples  (samples) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
   * parents  (parents) object 16B &#x27;SIRE&#x27; &#x27;DAM&#x27;
 Attributes:
-    comment:  Indices of parent samples with negative values indicating unkno...</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'parent'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-9a6e8e54-df69-457e-bce9-1018698c92e7' class='xr-array-in' type='checkbox' checked><label for='section-9a6e8e54-df69-457e-bce9-1018698c92e7' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>-1 -1 -1 -1 -1 -1 -1 -1 -1 ... 6463 3674 4278 6464 6465 1128 5128 6471</span></div><div class='xr-array-data'><pre>array([[  -1,   -1],
+    comment:  Indices of parent samples with negative values indicating unkno...</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'parent'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 6473</li><li><span class='xr-has-index'>parents</span>: 2</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-d7868cd5-1cf0-4d2b-81b3-dde253c224f0' class='xr-array-in' type='checkbox' checked><label for='section-d7868cd5-1cf0-4d2b-81b3-dde253c224f0' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>-1 -1 -1 -1 -1 -1 -1 -1 -1 ... 6463 3674 4278 6464 6465 1128 5128 6471</span></div><div class='xr-array-data'><pre>array([[  -1,   -1],
        [  -1,   -1],
        [  -1,   -1],
        ...,
        [4278, 6464],
        [6465, 1128],
-       [5128, 6471]])</pre></div></div></li><li class='xr-section-item'><input id='section-8361924b-6de4-4685-9f15-9aedf09d18d1' class='xr-section-summary-in' type='checkbox'  checked><label for='section-8361924b-6de4-4685-9f15-9aedf09d18d1' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-3b52ca17-eb01-479c-bf89-ca95865fc57d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3b52ca17-eb01-479c-bf89-ca95865fc57d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2e3bbef7-1d11-41ff-9718-7ccaf064003b' class='xr-var-data-in' type='checkbox'><label for='data-2e3bbef7-1d11-41ff-9718-7ccaf064003b' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-3cc341a0-9a1b-483d-8d4c-9c4c4a398747' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-3cc341a0-9a1b-483d-8d4c-9c4c4a398747' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-2310dcf6-91f1-43b5-bbd8-cb07ef7e8af7' class='xr-var-data-in' type='checkbox'><label for='data-2310dcf6-91f1-43b5-bbd8-cb07ef7e8af7' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-7e36c638-816f-45a0-8e82-72dcc802b92c' class='xr-section-summary-in' type='checkbox'  ><label for='section-7e36c638-816f-45a0-8e82-72dcc802b92c' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-4b4263ca-a903-4d3a-aeb8-1362fdbc5c64' class='xr-index-data-in' type='checkbox'/><label for='index-4b4263ca-a903-4d3a-aeb8-1362fdbc5c64' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+       [5128, 6471]])</pre></div></div></li><li class='xr-section-item'><input id='section-cf2aed29-63d1-4da2-abc4-c2488a2512ef' class='xr-section-summary-in' type='checkbox'  checked><label for='section-cf2aed29-63d1-4da2-abc4-c2488a2512ef' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-e320a0be-43e9-4d1c-963e-b8df74603f8d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e320a0be-43e9-4d1c-963e-b8df74603f8d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f6ae0ab8-e8f4-48c8-aa58-a0a8b77ec658' class='xr-var-data-in' type='checkbox'><label for='data-f6ae0ab8-e8f4-48c8-aa58-a0a8b77ec658' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>parents</span></div><div class='xr-var-dims'>(parents)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;SIRE&#x27; &#x27;DAM&#x27;</div><input id='attrs-cdf8edd0-2607-4a1d-86df-a4c237519d46' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-cdf8edd0-2607-4a1d-86df-a4c237519d46' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c9c5d4eb-82b5-4346-84b1-01edb28d7230' class='xr-var-data-in' type='checkbox'><label for='data-c9c5d4eb-82b5-4346-84b1-01edb28d7230' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-f728b97e-0e89-4b3c-9a53-fa3d545689c6' class='xr-section-summary-in' type='checkbox'  ><label for='section-f728b97e-0e89-4b3c-9a53-fa3d545689c6' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-57c5c0fa-a9c7-4c6e-a7f8-738b4c240bdf' class='xr-index-data-in' type='checkbox'/><label for='index-57c5c0fa-a9c7-4c6e-a7f8-738b4c240bdf' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-d7f2f187-95b9-4eee-b080-3af3ad86dbb9' class='xr-index-data-in' type='checkbox'/><label for='index-d7f2f187-95b9-4eee-b080-3af3ad86dbb9' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-d1193df3-ef21-494f-bca8-993886ba38ed' class='xr-section-summary-in' type='checkbox'  checked><label for='section-d1193df3-ef21-494f-bca8-993886ba38ed' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Indices of parent samples with negative values indicating unknown parents.</dd></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>parents</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-528f6d7d-d749-438e-8031-f199834926d0' class='xr-index-data-in' type='checkbox'/><label for='index-528f6d7d-d749-438e-8031-f199834926d0' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;SIRE&#x27;, &#x27;DAM&#x27;], dtype=&#x27;object&#x27;, name=&#x27;parents&#x27;))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-36844b7e-11f8-4140-ba27-fbc52a71dab8' class='xr-section-summary-in' type='checkbox'  checked><label for='section-36844b7e-11f8-4140-ba27-fbc52a71dab8' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Indices of parent samples with negative values indicating unknown parents.</dd></dl></div></li></ul></div></div></div></div>
 </div>
 <p>The <code class="docutils literal notranslate"><span class="pre">parent_id</span></code> matrix serves as a robust record of the pedigree structure which preserves the structure of a pedigree if the dataset is subset or reordered.
 The <code class="docutils literal notranslate"><span class="pre">parent</span></code> matrix contains integer indices of the parent samples within the dataset allowing for fast numerical calculations.
@@ -2366,7 +2366,7 @@ <h2>Pedigree relationships<a class="headerlink" href="#pedigree-relationships" t
 dask.array&lt;mul, shape=(6473, 6473), dtype=float64, chunksize=(6473, 6473), chunktype=numpy.ndarray&gt;
 Dimensions without coordinates: samples_0, samples_1
 Attributes:
-    comment:  Relationship matrix derived from pedigree structure.</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'stat_pedigree_relationship'</div><ul class='xr-dim-list'><li><span>samples_0</span>: 6473</li><li><span>samples_1</span>: 6473</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-154d7eea-07d9-4440-a875-fba7b16a4d97' class='xr-array-in' type='checkbox' checked><label for='section-154d7eea-07d9-4440-a875-fba7b16a4d97' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>dask.array&lt;chunksize=(6473, 6473), meta=np.ndarray&gt;</span></div><div class='xr-array-data'><table>
+    comment:  Relationship matrix derived from pedigree structure.</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'stat_pedigree_relationship'</div><ul class='xr-dim-list'><li><span>samples_0</span>: 6473</li><li><span>samples_1</span>: 6473</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-8e86f5fc-a19f-4ded-a25c-0c6841c85210' class='xr-array-in' type='checkbox' checked><label for='section-8e86f5fc-a19f-4ded-a25c-0c6841c85210' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>dask.array&lt;chunksize=(6473, 6473), meta=np.ndarray&gt;</span></div><div class='xr-array-data'><table>
     <tr>
         <td>
             <table style="border-collapse: collapse;">
@@ -2421,7 +2421,7 @@ <h2>Pedigree relationships<a class="headerlink" href="#pedigree-relationships" t
 </svg>
         </td>
     </tr>
-</table></div></div></li><li class='xr-section-item'><input id='section-1fe1d5c4-9d4c-4a43-918c-1028314f8430' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-1fe1d5c4-9d4c-4a43-918c-1028314f8430' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-f4d4aab5-e947-41a4-bcb1-dc55f81f6992' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-f4d4aab5-e947-41a4-bcb1-dc55f81f6992' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-3fa49b1b-920e-4ef8-bb68-c9f73e01b68a' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3fa49b1b-920e-4ef8-bb68-c9f73e01b68a' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Relationship matrix derived from pedigree structure.</dd></dl></div></li></ul></div></div></div></div>
+</table></div></div></li><li class='xr-section-item'><input id='section-ab425f55-b6d2-4f1a-9dbf-5e166e35b058' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-ab425f55-b6d2-4f1a-9dbf-5e166e35b058' class='xr-section-summary'  title='Expand/collapse section'>Coordinates: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-e586279c-ef7a-4306-9bdb-b79ac167a10b' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-e586279c-ef7a-4306-9bdb-b79ac167a10b' class='xr-section-summary'  title='Expand/collapse section'>Indexes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'></ul></div></li><li class='xr-section-item'><input id='section-ad37e162-2480-4cb7-b05f-cffaaab1725d' class='xr-section-summary-in' type='checkbox'  checked><label for='section-ad37e162-2480-4cb7-b05f-cffaaab1725d' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Relationship matrix derived from pedigree structure.</dd></dl></div></li></ul></div></div></div></div>
 </div>
 <p>Note that the dimensions of the matrices are called <code class="docutils literal notranslate"><span class="pre">samples_0</span></code> and <code class="docutils literal notranslate"><span class="pre">samples_1</span></code> to avoid using a single dimension twice in an xarray DataArray.
 Unfortunately, this means that the coordinates of the <code class="docutils literal notranslate"><span class="pre">samples</span></code> array have not been propagated to the new dimensions.
@@ -2827,7 +2827,7 @@ <h2>Pedigree relationships<a class="headerlink" href="#pedigree-relationships" t
   * samples_0  (samples_0) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
   * samples_1  (samples_1) object 52kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;6471&#x27; &#x27;6472&#x27; &#x27;6473&#x27;
 Attributes:
-    comment:  Relationship matrix derived from pedigree structure.</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'stat_pedigree_relationship'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples_0</span>: 6473</li><li><span class='xr-has-index'>samples_1</span>: 6473</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-62e326b6-3f56-4969-8e43-6bdde2fd42a1' class='xr-array-in' type='checkbox' checked><label for='section-62e326b6-3f56-4969-8e43-6bdde2fd42a1' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>1.0 0.0 0.0 0.0 0.0 0.0 ... 0.008972 0.02167 0.01508 0.5325 1.032</span></div><div class='xr-array-data'><pre>array([[1.        , 0.        , 0.        , ..., 0.015625  , 0.        ,
+    comment:  Relationship matrix derived from pedigree structure.</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'>'stat_pedigree_relationship'</div><ul class='xr-dim-list'><li><span class='xr-has-index'>samples_0</span>: 6473</li><li><span class='xr-has-index'>samples_1</span>: 6473</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-87bfc5f2-07ef-497d-bb0d-26370315c3bb' class='xr-array-in' type='checkbox' checked><label for='section-87bfc5f2-07ef-497d-bb0d-26370315c3bb' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>1.0 0.0 0.0 0.0 0.0 0.0 ... 0.008972 0.02167 0.01508 0.5325 1.032</span></div><div class='xr-array-data'><pre>array([[1.        , 0.        , 0.        , ..., 0.015625  , 0.        ,
         0.        ],
        [0.        , 1.        , 0.        , ..., 0.        , 0.        ,
         0.        ],
@@ -2839,15 +2839,15 @@ <h2>Pedigree relationships<a class="headerlink" href="#pedigree-relationships" t
        [0.        , 0.        , 0.        , ..., 0.01885986, 1.        ,
         0.5324707 ],
        [0.        , 0.        , 0.        , ..., 0.01507568, 0.5324707 ,
-        1.0324707 ]])</pre></div></div></li><li class='xr-section-item'><input id='section-b9f22c68-054e-4416-9729-c7ec6a69aa08' class='xr-section-summary-in' type='checkbox'  checked><label for='section-b9f22c68-054e-4416-9729-c7ec6a69aa08' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples_0</span></div><div class='xr-var-dims'>(samples_0)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-6ca1fb6b-b270-4798-9a69-38e6e46cb521' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-6ca1fb6b-b270-4798-9a69-38e6e46cb521' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-318acc70-4bea-4337-8113-0e9afce1b3d2' class='xr-var-data-in' type='checkbox'><label for='data-318acc70-4bea-4337-8113-0e9afce1b3d2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples_1</span></div><div class='xr-var-dims'>(samples_1)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-a807de17-b4b9-45d5-9907-3e4e712af76d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-a807de17-b4b9-45d5-9907-3e4e712af76d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-68f72a8b-05d0-4bd1-bebe-540b53280a4c' class='xr-var-data-in' type='checkbox'><label for='data-68f72a8b-05d0-4bd1-bebe-540b53280a4c' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-b612efcf-8fff-4ac0-9078-3823963ea485' class='xr-section-summary-in' type='checkbox'  ><label for='section-b612efcf-8fff-4ac0-9078-3823963ea485' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples_0</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-03b6c849-8133-4228-a143-cfa0afe49c9d' class='xr-index-data-in' type='checkbox'/><label for='index-03b6c849-8133-4228-a143-cfa0afe49c9d' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+        1.0324707 ]])</pre></div></div></li><li class='xr-section-item'><input id='section-db37c4b8-6bbf-4c75-bcd4-fa99da47877d' class='xr-section-summary-in' type='checkbox'  checked><label for='section-db37c4b8-6bbf-4c75-bcd4-fa99da47877d' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples_0</span></div><div class='xr-var-dims'>(samples_0)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-c4ecdfab-e26b-446e-b214-570dff767c0a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c4ecdfab-e26b-446e-b214-570dff767c0a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c1c5ee39-4574-4149-a987-6adf4576c55f' class='xr-var-data-in' type='checkbox'><label for='data-c1c5ee39-4574-4149-a987-6adf4576c55f' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples_1</span></div><div class='xr-var-dims'>(samples_1)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;6472&#x27; &#x27;6473&#x27;</div><input id='attrs-889a3294-5560-4139-a914-f47052d92205' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-889a3294-5560-4139-a914-f47052d92205' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-bb9cb39e-88af-4f5d-883e-af204f41cab9' class='xr-var-data-in' type='checkbox'><label for='data-bb9cb39e-88af-4f5d-883e-af204f41cab9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;6471&#x27;, &#x27;6472&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-49de1e25-fc91-49ea-9a01-9734d723089d' class='xr-section-summary-in' type='checkbox'  ><label for='section-49de1e25-fc91-49ea-9a01-9734d723089d' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples_0</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-da6a39c4-0db5-4eed-aa58-2d5858c9f935' class='xr-index-data-in' type='checkbox'/><label for='index-da6a39c4-0db5-4eed-aa58-2d5858c9f935' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples_0&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>samples_1</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-1a2f17f5-187b-48b4-985d-d244dfd044a4' class='xr-index-data-in' type='checkbox'/><label for='index-1a2f17f5-187b-48b4-985d-d244dfd044a4' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+      dtype=&#x27;object&#x27;, name=&#x27;samples_0&#x27;, length=6473))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>samples_1</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-f4262b69-f01c-4178-b8b9-0dc3fc6e8258' class='xr-index-data-in' type='checkbox'/><label for='index-f4262b69-f01c-4178-b8b9-0dc3fc6e8258' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6472&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples_1&#x27;, length=6473))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-8e7a6677-e3c0-4477-9f25-480bc4f17900' class='xr-section-summary-in' type='checkbox'  checked><label for='section-8e7a6677-e3c0-4477-9f25-480bc4f17900' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Relationship matrix derived from pedigree structure.</dd></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples_1&#x27;, length=6473))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-119c959a-2f6f-4c56-9431-8fe702424a72' class='xr-section-summary-in' type='checkbox'  checked><label for='section-119c959a-2f6f-4c56-9431-8fe702424a72' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>comment :</span></dt><dd>Relationship matrix derived from pedigree structure.</dd></dl></div></li></ul></div></div></div></div>
 </div>
 <p>We can plot the relationship using matplotlib.</p>
 <div class="cell docutils container">
@@ -3459,20 +3459,20 @@ <h2>Genomic relationships<a class="headerlink" href="#genomic-relationships" tit
        [2., 1., 1., ..., 0., 2., 0.]])
 Coordinates:
   * variants  (variants) object 8kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;997&#x27; &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;
-  * samples   (samples) object 28kB &#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6470&#x27; &#x27;6471&#x27; &#x27;6473&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>variants</span>: 1000</li><li><span class='xr-has-index'>samples</span>: 3534</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-b713d955-64d1-4b6a-8796-87e8deda0794' class='xr-array-in' type='checkbox' checked><label for='section-b713d955-64d1-4b6a-8796-87e8deda0794' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>1.0 0.0 2.0 1.0 0.0 1.0 0.0 1.0 ... 1.0 2.0 2.0 1.0 0.0 0.0 2.0 0.0</span></div><div class='xr-array-data'><pre>array([[1., 0., 2., ..., 0., 1., 0.],
+  * samples   (samples) object 28kB &#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6470&#x27; &#x27;6471&#x27; &#x27;6473&#x27;</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.DataArray</div><div class='xr-array-name'></div><ul class='xr-dim-list'><li><span class='xr-has-index'>variants</span>: 1000</li><li><span class='xr-has-index'>samples</span>: 3534</li></ul></div><ul class='xr-sections'><li class='xr-section-item'><div class='xr-array-wrap'><input id='section-00a5525b-10e6-4e77-90e3-f2845b9d689a' class='xr-array-in' type='checkbox' checked><label for='section-00a5525b-10e6-4e77-90e3-f2845b9d689a' title='Show/hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-array-preview xr-preview'><span>1.0 0.0 2.0 1.0 0.0 1.0 0.0 1.0 ... 1.0 2.0 2.0 1.0 0.0 0.0 2.0 0.0</span></div><div class='xr-array-data'><pre>array([[1., 0., 2., ..., 0., 1., 0.],
        [1., 2., 2., ..., 1., 1., 2.],
        [1., 1., 0., ..., 1., 2., 2.],
        ...,
        [2., 0., 1., ..., 0., 0., 0.],
        [2., 2., 2., ..., 2., 2., 2.],
-       [2., 1., 1., ..., 0., 2., 0.]])</pre></div></div></li><li class='xr-section-item'><input id='section-0e075399-5539-4a1c-8457-bcc83cc52ff0' class='xr-section-summary-in' type='checkbox'  checked><label for='section-0e075399-5539-4a1c-8457-bcc83cc52ff0' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>variants</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;</div><input id='attrs-c9944e24-945e-4230-b8fc-afa4d614617d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c9944e24-945e-4230-b8fc-afa4d614617d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-19740b1d-1f60-4fdf-b122-699d821e08cb' class='xr-var-data-in' type='checkbox'><label for='data-19740b1d-1f60-4fdf-b122-699d821e08cb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-89083210-78e2-4916-918c-8b98286a9c94' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-89083210-78e2-4916-918c-8b98286a9c94' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-902d1147-98d2-456f-9d03-9e7ffe034071' class='xr-var-data-in' type='checkbox'><label for='data-902d1147-98d2-456f-9d03-9e7ffe034071' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-9283eeab-24ed-4eee-8ac8-cc4d3d233b2d' class='xr-section-summary-in' type='checkbox'  ><label for='section-9283eeab-24ed-4eee-8ac8-cc4d3d233b2d' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>variants</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-1c7e74af-d7b3-4058-afde-eeb4b6c0125a' class='xr-index-data-in' type='checkbox'/><label for='index-1c7e74af-d7b3-4058-afde-eeb4b6c0125a' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+       [2., 1., 1., ..., 0., 2., 0.]])</pre></div></div></li><li class='xr-section-item'><input id='section-3165783b-a67f-4926-86c7-e5f6866cafc5' class='xr-section-summary-in' type='checkbox'  checked><label for='section-3165783b-a67f-4926-86c7-e5f6866cafc5' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>variants</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;</div><input id='attrs-e812b9b6-c441-421d-81bb-12a21e7e273d' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e812b9b6-c441-421d-81bb-12a21e7e273d' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-71eb4d84-25fd-444f-b23d-be1efc9e60f2' class='xr-var-data-in' type='checkbox'><label for='data-71eb4d84-25fd-444f-b23d-be1efc9e60f2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-16b805e5-32e1-43b0-9f61-4cc8f29e49ce' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-16b805e5-32e1-43b0-9f61-4cc8f29e49ce' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-daa975b8-c243-48a6-97c7-b134b60951d4' class='xr-var-data-in' type='checkbox'><label for='data-daa975b8-c243-48a6-97c7-b134b60951d4' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-a065a798-3140-4cd8-bcc9-bda2c93e3978' class='xr-section-summary-in' type='checkbox'  ><label for='section-a065a798-3140-4cd8-bcc9-bda2c93e3978' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>variants</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-d51e1a5a-2290-4207-9793-3480af93357a' class='xr-index-data-in' type='checkbox'/><label for='index-d51e1a5a-2290-4207-9793-3480af93357a' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;991&#x27;, &#x27;992&#x27;, &#x27;993&#x27;, &#x27;994&#x27;, &#x27;995&#x27;, &#x27;996&#x27;, &#x27;997&#x27;, &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;variants&#x27;, length=1000))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-8c66773e-0843-421b-867a-b942c336a0c4' class='xr-index-data-in' type='checkbox'/><label for='index-8c66773e-0843-421b-867a-b942c336a0c4' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, &#x27;588&#x27;, &#x27;589&#x27;, &#x27;590&#x27;, &#x27;591&#x27;, &#x27;592&#x27;, &#x27;593&#x27;, &#x27;594&#x27;,
+      dtype=&#x27;object&#x27;, name=&#x27;variants&#x27;, length=1000))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-3a999dee-a139-4031-bc74-a2011cac9efb' class='xr-index-data-in' type='checkbox'/><label for='index-3a999dee-a139-4031-bc74-a2011cac9efb' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, &#x27;588&#x27;, &#x27;589&#x27;, &#x27;590&#x27;, &#x27;591&#x27;, &#x27;592&#x27;, &#x27;593&#x27;, &#x27;594&#x27;,
        ...
        &#x27;6463&#x27;, &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=3534))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-33fda55b-8267-4695-809c-956ef7fa1728' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-33fda55b-8267-4695-809c-956ef7fa1728' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=3534))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-05cb4639-502e-457f-84a5-c020baee8025' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-05cb4639-502e-457f-84a5-c020baee8025' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
 </div>
 <p>Next we create a dataset containing the <code class="docutils literal notranslate"><span class="pre">call_dosage</span></code> and <code class="docutils literal notranslate"><span class="pre">sample_id</span></code> variables.</p>
 <div class="cell docutils container">
@@ -3856,20 +3856,20 @@ <h2>Genomic relationships<a class="headerlink" href="#genomic-relationships" tit
   * variants     (variants) object 8kB &#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; &#x27;4&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;
 Data variables:
     sample_id    (samples) object 28kB &#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;
-    call_dosage  (variants, samples) float64 28MB 1.0 0.0 2.0 ... 0.0 2.0 0.0</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-3801da66-b4ae-4716-806b-b3da2bc58f22' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-3801da66-b4ae-4716-806b-b3da2bc58f22' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 3534</li><li><span class='xr-has-index'>variants</span>: 1000</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-29855d7b-7e62-411a-97e4-6ab43d08d0ae' class='xr-section-summary-in' type='checkbox'  checked><label for='section-29855d7b-7e62-411a-97e4-6ab43d08d0ae' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-955a1bab-966d-4c53-bc2b-fbb67be84ca0' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-955a1bab-966d-4c53-bc2b-fbb67be84ca0' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0fc4a747-da60-4475-9b88-b461d6f0c1cb' class='xr-var-data-in' type='checkbox'><label for='data-0fc4a747-da60-4475-9b88-b461d6f0c1cb' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>variants</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;</div><input id='attrs-0180afa0-fc60-4cc9-9a41-9bfe746d737a' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-0180afa0-fc60-4cc9-9a41-9bfe746d737a' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7d3ca224-23f1-4fcd-9b6f-4194037825b1' class='xr-var-data-in' type='checkbox'><label for='data-7d3ca224-23f1-4fcd-9b6f-4194037825b1' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-58d58eb2-4a0c-4ee8-a63f-92ab522eba25' class='xr-section-summary-in' type='checkbox'  checked><label for='section-58d58eb2-4a0c-4ee8-a63f-92ab522eba25' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-2416bbef-fac4-4311-b8a3-2cbdd301cba3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-2416bbef-fac4-4311-b8a3-2cbdd301cba3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-4120457f-f8ee-4f4d-ad06-0d8046384480' class='xr-var-data-in' type='checkbox'><label for='data-4120457f-f8ee-4f4d-ad06-0d8046384480' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>1.0 0.0 2.0 1.0 ... 0.0 0.0 2.0 0.0</div><input id='attrs-ce3d035b-6b89-4d83-95b7-182f48662005' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-ce3d035b-6b89-4d83-95b7-182f48662005' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-a9819d73-ef0e-4e3a-9440-3cc698dd7ee6' class='xr-var-data-in' type='checkbox'><label for='data-a9819d73-ef0e-4e3a-9440-3cc698dd7ee6' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([[1., 0., 2., ..., 0., 1., 0.],
+    call_dosage  (variants, samples) float64 28MB 1.0 0.0 2.0 ... 0.0 2.0 0.0</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-83daecb5-1c2c-4127-b1d0-7f88649a9367' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-83daecb5-1c2c-4127-b1d0-7f88649a9367' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>samples</span>: 3534</li><li><span class='xr-has-index'>variants</span>: 1000</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-5e345ef5-88b5-4526-a5ae-b381c5dc9ef6' class='xr-section-summary-in' type='checkbox'  checked><label for='section-5e345ef5-88b5-4526-a5ae-b381c5dc9ef6' class='xr-section-summary' >Coordinates: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>samples</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-c5c56c5c-d115-48d5-b1c3-2a7bd91f3e91' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-c5c56c5c-d115-48d5-b1c3-2a7bd91f3e91' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d326c30a-5bda-4e15-9d45-642dc2023cf2' class='xr-var-data-in' type='checkbox'><label for='data-d326c30a-5bda-4e15-9d45-642dc2023cf2' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>variants</span></div><div class='xr-var-dims'>(variants)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;1&#x27; &#x27;2&#x27; &#x27;3&#x27; ... &#x27;998&#x27; &#x27;999&#x27; &#x27;1000&#x27;</div><input id='attrs-e79194bb-01f8-46cc-8080-b8e6771f401b' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-e79194bb-01f8-46cc-8080-b8e6771f401b' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-b087b469-1994-4ee0-a34d-21e532c74848' class='xr-var-data-in' type='checkbox'><label for='data-b087b469-1994-4ee0-a34d-21e532c74848' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, ..., &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;], dtype=object)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-f5ebafbd-1862-4d1d-80b2-fbea1ebad440' class='xr-section-summary-in' type='checkbox'  checked><label for='section-f5ebafbd-1862-4d1d-80b2-fbea1ebad440' class='xr-section-summary' >Data variables: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>sample_id</span></div><div class='xr-var-dims'>(samples)</div><div class='xr-var-dtype'>object</div><div class='xr-var-preview xr-preview'>&#x27;584&#x27; &#x27;585&#x27; &#x27;587&#x27; ... &#x27;6471&#x27; &#x27;6473&#x27;</div><input id='attrs-828b04a7-e923-46c8-a2ac-df1092d22d6c' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-828b04a7-e923-46c8-a2ac-df1092d22d6c' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0f7d980f-542a-4100-9994-7727a03b6a16' class='xr-var-data-in' type='checkbox'><label for='data-0f7d980f-542a-4100-9994-7727a03b6a16' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, ..., &#x27;6470&#x27;, &#x27;6471&#x27;, &#x27;6473&#x27;], dtype=object)</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span>call_dosage</span></div><div class='xr-var-dims'>(variants, samples)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>1.0 0.0 2.0 1.0 ... 0.0 0.0 2.0 0.0</div><input id='attrs-7c4dfcc3-ec9e-42d2-a20f-aff2a13a74d3' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-7c4dfcc3-ec9e-42d2-a20f-aff2a13a74d3' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-59b86382-b7fa-415c-b772-6d391a7db208' class='xr-var-data-in' type='checkbox'><label for='data-59b86382-b7fa-415c-b772-6d391a7db208' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([[1., 0., 2., ..., 0., 1., 0.],
        [1., 2., 2., ..., 1., 1., 2.],
        [1., 1., 0., ..., 1., 2., 2.],
        ...,
        [2., 0., 1., ..., 0., 0., 0.],
        [2., 2., 2., ..., 2., 2., 2.],
-       [2., 1., 1., ..., 0., 2., 0.]])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-d234b2c4-05f5-4636-a759-a531a63c45d8' class='xr-section-summary-in' type='checkbox'  ><label for='section-d234b2c4-05f5-4636-a759-a531a63c45d8' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-c618f650-15c8-493a-a6ac-22560169dff9' class='xr-index-data-in' type='checkbox'/><label for='index-c618f650-15c8-493a-a6ac-22560169dff9' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, &#x27;588&#x27;, &#x27;589&#x27;, &#x27;590&#x27;, &#x27;591&#x27;, &#x27;592&#x27;, &#x27;593&#x27;, &#x27;594&#x27;,
+       [2., 1., 1., ..., 0., 2., 0.]])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-187185fc-8bf2-4e54-9427-f8fcc9272cb3' class='xr-section-summary-in' type='checkbox'  ><label for='section-187185fc-8bf2-4e54-9427-f8fcc9272cb3' class='xr-section-summary' >Indexes: <span>(2)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-index-name'><div>samples</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-c6f7d09e-bf59-4342-9faa-a8c0de19bd79' class='xr-index-data-in' type='checkbox'/><label for='index-c6f7d09e-bf59-4342-9faa-a8c0de19bd79' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;584&#x27;, &#x27;585&#x27;, &#x27;587&#x27;, &#x27;588&#x27;, &#x27;589&#x27;, &#x27;590&#x27;, &#x27;591&#x27;, &#x27;592&#x27;, &#x27;593&#x27;, &#x27;594&#x27;,
        ...
        &#x27;6463&#x27;, &#x27;6464&#x27;, &#x27;6465&#x27;, &#x27;6466&#x27;, &#x27;6467&#x27;, &#x27;6468&#x27;, &#x27;6469&#x27;, &#x27;6470&#x27;, &#x27;6471&#x27;,
        &#x27;6473&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=3534))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>variants</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-e5ab2662-a0d5-40bf-a755-969770fdc1bd' class='xr-index-data-in' type='checkbox'/><label for='index-e5ab2662-a0d5-40bf-a755-969770fdc1bd' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
+      dtype=&#x27;object&#x27;, name=&#x27;samples&#x27;, length=3534))</pre></div></li><li class='xr-var-item'><div class='xr-index-name'><div>variants</div></div><div class='xr-index-preview'>PandasIndex</div><div></div><input id='index-830cbf7c-5ec8-4d17-b4e0-cef6f68716f7' class='xr-index-data-in' type='checkbox'/><label for='index-830cbf7c-5ec8-4d17-b4e0-cef6f68716f7' title='Show/Hide index repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-index-data'><pre>PandasIndex(Index([&#x27;1&#x27;, &#x27;2&#x27;, &#x27;3&#x27;, &#x27;4&#x27;, &#x27;5&#x27;, &#x27;6&#x27;, &#x27;7&#x27;, &#x27;8&#x27;, &#x27;9&#x27;, &#x27;10&#x27;,
        ...
        &#x27;991&#x27;, &#x27;992&#x27;, &#x27;993&#x27;, &#x27;994&#x27;, &#x27;995&#x27;, &#x27;996&#x27;, &#x27;997&#x27;, &#x27;998&#x27;, &#x27;999&#x27;, &#x27;1000&#x27;],
-      dtype=&#x27;object&#x27;, name=&#x27;variants&#x27;, length=1000))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-2c27acca-ab7c-4b49-aa32-a8c76a989503' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-2c27acca-ab7c-4b49-aa32-a8c76a989503' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
+      dtype=&#x27;object&#x27;, name=&#x27;variants&#x27;, length=1000))</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-6cec6a0b-2351-4410-bb4e-9d67009befaa' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-6cec6a0b-2351-4410-bb4e-9d67009befaa' class='xr-section-summary'  title='Expand/collapse section'>Attributes: <span>(0)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'></dl></div></li></ul></div></div></div></div>
 </div>
 </section>
 <section id="the-vanraden-grm">
@@ -3951,7 +3951,7 @@ <h2>The VanRaden GRM<a class="headerlink" href="#the-vanraden-grm" title="Permal
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2802/892134664.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2704/892134664.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims[&quot;samples&quot;])
 </pre></div>
 </div>
@@ -4055,7 +4055,7 @@ <h2>A better estimate of ancestral allele frequencies<a class="headerlink" href=
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2802/3477141311.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2704/3477141311.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims[&quot;samples&quot;])
 </pre></div>
 </div>
@@ -4127,7 +4127,7 @@ <h2>Weir-Goudet GRM<a class="headerlink" href="#weir-goudet-grm" title="Permalin
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2802/70656024.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/tmp/ipykernel_2704/70656024.py:1: FutureWarning: The return type of `Dataset.dims` will be changed to return a set of dimension names in future, in order to be more consistent with `DataArray.dims`. To access a mapping from dimension names to lengths, please use `Dataset.sizes`.
   tril_idx = np.tril_indices(gen.dims[&quot;samples&quot;])
 </pre></div>
 </div>
diff --git a/latest/generated/sgkit.variables.call_dosage_spec.html b/latest/generated/sgkit.variables.call_dosage_spec.html
index c466e461f..6146bde64 100644
--- a/latest/generated/sgkit.variables.call_dosage_spec.html
+++ b/latest/generated/sgkit.variables.call_dosage_spec.html
@@ -748,7 +748,7 @@
 <h1>sgkit.variables.call_dosage_spec<a class="headerlink" href="#sgkit-variables-call-dosage-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.call_dosage_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">call_dosage_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='call_dosage',</span> <span class="pre">__doc__='\nDosages,</span> <span class="pre">encoded</span> <span class="pre">as</span> <span class="pre">floats,</span> <span class="pre">with</span> <span class="pre">NaN</span> <span class="pre">indicating</span> <span class="pre">a</span> <span class="pre">missing</span> <span class="pre">value.\nDosages</span> <span class="pre">can</span> <span class="pre">represent</span> <span class="pre">one</span> <span class="pre">of</span> <span class="pre">several</span> <span class="pre">possible</span> <span class="pre">quantities,</span> <span class="pre">e.g.:\n-</span> <span class="pre">Alternate</span> <span class="pre">allele</span> <span class="pre">counts\n-</span> <span class="pre">Recessive</span> <span class="pre">or</span> <span class="pre">dominant</span> <span class="pre">allele</span> <span class="pre">encodings\n-</span> <span class="pre">True</span> <span class="pre">dosages</span> <span class="pre">as</span> <span class="pre">computed</span> <span class="pre">from</span> <span class="pre">imputed</span> <span class="pre">or</span> <span class="pre">probabilistic</span> <span class="pre">variant</span> <span class="pre">calls\n-</span> <span class="pre">Any</span> <span class="pre">other</span> <span class="pre">custom</span> <span class="pre">encoding</span> <span class="pre">in</span> <span class="pre">a</span> <span class="pre">user-defined</span> <span class="pre">variable\n',</span> <span class="pre">kind={'u',</span> <span class="pre">'i',</span> <span class="pre">'f'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('variants',</span> <span class="pre">'samples'))</span></em><a class="headerlink" href="#sgkit.variables.call_dosage_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">call_dosage_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='call_dosage',</span> <span class="pre">__doc__='\nDosages,</span> <span class="pre">encoded</span> <span class="pre">as</span> <span class="pre">floats,</span> <span class="pre">with</span> <span class="pre">NaN</span> <span class="pre">indicating</span> <span class="pre">a</span> <span class="pre">missing</span> <span class="pre">value.\nDosages</span> <span class="pre">can</span> <span class="pre">represent</span> <span class="pre">one</span> <span class="pre">of</span> <span class="pre">several</span> <span class="pre">possible</span> <span class="pre">quantities,</span> <span class="pre">e.g.:\n-</span> <span class="pre">Alternate</span> <span class="pre">allele</span> <span class="pre">counts\n-</span> <span class="pre">Recessive</span> <span class="pre">or</span> <span class="pre">dominant</span> <span class="pre">allele</span> <span class="pre">encodings\n-</span> <span class="pre">True</span> <span class="pre">dosages</span> <span class="pre">as</span> <span class="pre">computed</span> <span class="pre">from</span> <span class="pre">imputed</span> <span class="pre">or</span> <span class="pre">probabilistic</span> <span class="pre">variant</span> <span class="pre">calls\n-</span> <span class="pre">Any</span> <span class="pre">other</span> <span class="pre">custom</span> <span class="pre">encoding</span> <span class="pre">in</span> <span class="pre">a</span> <span class="pre">user-defined</span> <span class="pre">variable\n',</span> <span class="pre">kind={'f',</span> <span class="pre">'i',</span> <span class="pre">'u'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('variants',</span> <span class="pre">'samples'))</span></em><a class="headerlink" href="#sgkit.variables.call_dosage_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Dosages, encoded as floats, with NaN indicating a missing value.
 Dosages can represent one of several possible quantities, e.g.:
 - Alternate allele counts
diff --git a/latest/generated/sgkit.variables.interval_contig_name_spec.html b/latest/generated/sgkit.variables.interval_contig_name_spec.html
index 2b1728a76..621533931 100644
--- a/latest/generated/sgkit.variables.interval_contig_name_spec.html
+++ b/latest/generated/sgkit.variables.interval_contig_name_spec.html
@@ -748,7 +748,7 @@
 <h1>sgkit.variables.interval_contig_name_spec<a class="headerlink" href="#sgkit-variables-interval-contig-name-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.interval_contig_name_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">interval_contig_name_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='interval_contig_name',</span> <span class="pre">__doc__='Interval</span> <span class="pre">contig</span> <span class="pre">name.</span> <span class="pre">Must</span> <span class="pre">match</span> <span class="pre">a</span> <span class="pre">contig</span> <span class="pre">defined</span> <span class="pre">in</span> <span class="pre">the</span> <span class="pre">``contigs``</span> <span class="pre">attribute.',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=None)</span></em><a class="headerlink" href="#sgkit.variables.interval_contig_name_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">interval_contig_name_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='interval_contig_name',</span> <span class="pre">__doc__='Interval</span> <span class="pre">contig</span> <span class="pre">name.</span> <span class="pre">Must</span> <span class="pre">match</span> <span class="pre">a</span> <span class="pre">contig</span> <span class="pre">defined</span> <span class="pre">in</span> <span class="pre">the</span> <span class="pre">``contigs``</span> <span class="pre">attribute.',</span> <span class="pre">kind={'U',</span> <span class="pre">'S',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=None)</span></em><a class="headerlink" href="#sgkit.variables.interval_contig_name_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Interval contig name. Must match a contig defined in the <code class="docutils literal notranslate"><span class="pre">contigs</span></code> attribute.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.parent_id_spec.html b/latest/generated/sgkit.variables.parent_id_spec.html
index 9c396177b..292cd9dcd 100644
--- a/latest/generated/sgkit.variables.parent_id_spec.html
+++ b/latest/generated/sgkit.variables.parent_id_spec.html
@@ -748,7 +748,7 @@
 <h1>sgkit.variables.parent_id_spec<a class="headerlink" href="#sgkit-variables-parent-id-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.parent_id_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">parent_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='parent_id',</span> <span class="pre">__doc__='\nUnique</span> <span class="pre">identifiers</span> <span class="pre">of</span> <span class="pre">parent</span> <span class="pre">samples</span> <span class="pre">matching</span> <span class="pre">those</span> <span class="pre">in\n:data:`sgkit.variables.sample_id_spec`.\n',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('samples',</span> <span class="pre">'parents'))</span></em><a class="headerlink" href="#sgkit.variables.parent_id_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">parent_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='parent_id',</span> <span class="pre">__doc__='\nUnique</span> <span class="pre">identifiers</span> <span class="pre">of</span> <span class="pre">parent</span> <span class="pre">samples</span> <span class="pre">matching</span> <span class="pre">those</span> <span class="pre">in\n:data:`sgkit.variables.sample_id_spec`.\n',</span> <span class="pre">kind={'U',</span> <span class="pre">'S',</span> <span class="pre">'O'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('samples',</span> <span class="pre">'parents'))</span></em><a class="headerlink" href="#sgkit.variables.parent_id_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Unique identifiers of parent samples matching those in
 <a class="reference internal" href="sgkit.variables.sample_id_spec.html#sgkit.variables.sample_id_spec" title="sgkit.variables.sample_id_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.sample_id_spec</span></code></a>.</p>
 </dd></dl>
diff --git a/latest/generated/sgkit.variables.sample_id_spec.html b/latest/generated/sgkit.variables.sample_id_spec.html
index 8ec412a23..6bc6ff4d0 100644
--- a/latest/generated/sgkit.variables.sample_id_spec.html
+++ b/latest/generated/sgkit.variables.sample_id_spec.html
@@ -748,7 +748,7 @@
 <h1>sgkit.variables.sample_id_spec<a class="headerlink" href="#sgkit-variables-sample-id-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.sample_id_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">sample_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='sample_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">sample.',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('samples',))</span></em><a class="headerlink" href="#sgkit.variables.sample_id_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">sample_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='sample_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">sample.',</span> <span class="pre">kind={'U',</span> <span class="pre">'S',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('samples',))</span></em><a class="headerlink" href="#sgkit.variables.sample_id_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>The unique identifier of the sample.</p>
 </dd></dl>
 
diff --git a/latest/generated/sgkit.variables.traits_spec.html b/latest/generated/sgkit.variables.traits_spec.html
index 580adf33f..dafb0b3aa 100644
--- a/latest/generated/sgkit.variables.traits_spec.html
+++ b/latest/generated/sgkit.variables.traits_spec.html
@@ -748,7 +748,7 @@
 <h1>sgkit.variables.traits_spec<a class="headerlink" href="#sgkit-variables-traits-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.traits_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">traits_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='traits',</span> <span class="pre">__doc__='\nTrait</span> <span class="pre">(for</span> <span class="pre">example</span> <span class="pre">phenotype)</span> <span class="pre">variable</span> <span class="pre">names.</span> <span class="pre">Must</span> <span class="pre">all</span> <span class="pre">be</span> <span class="pre">continuous</span> <span class="pre">and\ncorrespond</span> <span class="pre">to</span> <span class="pre">1</span> <span class="pre">or</span> <span class="pre">2D</span> <span class="pre">dataset</span> <span class="pre">variables</span> <span class="pre">of</span> <span class="pre">shape</span> <span class="pre">(samples[,</span> <span class="pre">traits]).\n2D</span> <span class="pre">trait</span> <span class="pre">arrays</span> <span class="pre">will</span> <span class="pre">be</span> <span class="pre">assumed</span> <span class="pre">to</span> <span class="pre">contain</span> <span class="pre">separate</span> <span class="pre">traits</span> <span class="pre">within</span> <span class="pre">columns\nand</span> <span class="pre">concatenated</span> <span class="pre">to</span> <span class="pre">any</span> <span class="pre">1D</span> <span class="pre">traits</span> <span class="pre">along</span> <span class="pre">the</span> <span class="pre">second</span> <span class="pre">axis</span> <span class="pre">(columns).\n',</span> <span class="pre">kind=None,</span> <span class="pre">ndim={1,</span> <span class="pre">2},</span> <span class="pre">dims=('samples',</span> <span class="pre">{None,</span> <span class="pre">'*'}))</span></em><a class="headerlink" href="#sgkit.variables.traits_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">traits_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='traits',</span> <span class="pre">__doc__='\nTrait</span> <span class="pre">(for</span> <span class="pre">example</span> <span class="pre">phenotype)</span> <span class="pre">variable</span> <span class="pre">names.</span> <span class="pre">Must</span> <span class="pre">all</span> <span class="pre">be</span> <span class="pre">continuous</span> <span class="pre">and\ncorrespond</span> <span class="pre">to</span> <span class="pre">1</span> <span class="pre">or</span> <span class="pre">2D</span> <span class="pre">dataset</span> <span class="pre">variables</span> <span class="pre">of</span> <span class="pre">shape</span> <span class="pre">(samples[,</span> <span class="pre">traits]).\n2D</span> <span class="pre">trait</span> <span class="pre">arrays</span> <span class="pre">will</span> <span class="pre">be</span> <span class="pre">assumed</span> <span class="pre">to</span> <span class="pre">contain</span> <span class="pre">separate</span> <span class="pre">traits</span> <span class="pre">within</span> <span class="pre">columns\nand</span> <span class="pre">concatenated</span> <span class="pre">to</span> <span class="pre">any</span> <span class="pre">1D</span> <span class="pre">traits</span> <span class="pre">along</span> <span class="pre">the</span> <span class="pre">second</span> <span class="pre">axis</span> <span class="pre">(columns).\n',</span> <span class="pre">kind=None,</span> <span class="pre">ndim={1,</span> <span class="pre">2},</span> <span class="pre">dims=('samples',</span> <span class="pre">{'*',</span> <span class="pre">None}))</span></em><a class="headerlink" href="#sgkit.variables.traits_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Trait (for example phenotype) variable names. Must all be continuous and
 correspond to 1 or 2D dataset variables of shape (samples[, traits]).
 2D trait arrays will be assumed to contain separate traits within columns
diff --git a/latest/generated/sgkit.variables.variant_contig_spec.html b/latest/generated/sgkit.variables.variant_contig_spec.html
index c579554a6..a768ee167 100644
--- a/latest/generated/sgkit.variables.variant_contig_spec.html
+++ b/latest/generated/sgkit.variables.variant_contig_spec.html
@@ -748,7 +748,7 @@
 <h1>sgkit.variables.variant_contig_spec<a class="headerlink" href="#sgkit-variables-variant-contig-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.variant_contig_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_contig_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='variant_contig',</span> <span class="pre">__doc__='\nIndex</span> <span class="pre">corresponding</span> <span class="pre">to</span> <span class="pre">contig</span> <span class="pre">name</span> <span class="pre">for</span> <span class="pre">each</span> <span class="pre">variant.</span> <span class="pre">In</span> <span class="pre">some</span> <span class="pre">less</span> <span class="pre">common\nscenarios,</span> <span class="pre">this</span> <span class="pre">may</span> <span class="pre">also</span> <span class="pre">be</span> <span class="pre">equivalent</span> <span class="pre">to</span> <span class="pre">the</span> <span class="pre">contig</span> <span class="pre">names</span> <span class="pre">if</span> <span class="pre">the</span> <span class="pre">data\ngenerating</span> <span class="pre">process</span> <span class="pre">used</span> <span class="pre">contig</span> <span class="pre">names</span> <span class="pre">that</span> <span class="pre">were</span> <span class="pre">also</span> <span class="pre">integers.\n',</span> <span class="pre">kind={'u',</span> <span class="pre">'i'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('variants',))</span></em><a class="headerlink" href="#sgkit.variables.variant_contig_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_contig_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='variant_contig',</span> <span class="pre">__doc__='\nIndex</span> <span class="pre">corresponding</span> <span class="pre">to</span> <span class="pre">contig</span> <span class="pre">name</span> <span class="pre">for</span> <span class="pre">each</span> <span class="pre">variant.</span> <span class="pre">In</span> <span class="pre">some</span> <span class="pre">less</span> <span class="pre">common\nscenarios,</span> <span class="pre">this</span> <span class="pre">may</span> <span class="pre">also</span> <span class="pre">be</span> <span class="pre">equivalent</span> <span class="pre">to</span> <span class="pre">the</span> <span class="pre">contig</span> <span class="pre">names</span> <span class="pre">if</span> <span class="pre">the</span> <span class="pre">data\ngenerating</span> <span class="pre">process</span> <span class="pre">used</span> <span class="pre">contig</span> <span class="pre">names</span> <span class="pre">that</span> <span class="pre">were</span> <span class="pre">also</span> <span class="pre">integers.\n',</span> <span class="pre">kind={'i',</span> <span class="pre">'u'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('variants',))</span></em><a class="headerlink" href="#sgkit.variables.variant_contig_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</p>
diff --git a/latest/generated/sgkit.variables.variant_genotype_count_spec.html b/latest/generated/sgkit.variables.variant_genotype_count_spec.html
index 961d12c64..dff3aa806 100644
--- a/latest/generated/sgkit.variables.variant_genotype_count_spec.html
+++ b/latest/generated/sgkit.variables.variant_genotype_count_spec.html
@@ -748,7 +748,7 @@
 <h1>sgkit.variables.variant_genotype_count_spec<a class="headerlink" href="#sgkit-variables-variant-genotype-count-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.variant_genotype_count_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_genotype_count_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='variant_genotype_count',</span> <span class="pre">__doc__='\nThe</span> <span class="pre">number</span> <span class="pre">of</span> <span class="pre">observations</span> <span class="pre">for</span> <span class="pre">each</span> <span class="pre">possible</span> <span class="pre">genotype</span> <span class="pre">at</span> <span class="pre">each</span> <span class="pre">variant.\nCounts</span> <span class="pre">are</span> <span class="pre">sorted</span> <span class="pre">following</span> <span class="pre">the</span> <span class="pre">ordering</span> <span class="pre">defined</span> <span class="pre">in</span> <span class="pre">the</span> <span class="pre">VCF</span> <span class="pre">specification.\n\n-</span> <span class="pre">For</span> <span class="pre">biallelic,</span> <span class="pre">diploid</span> <span class="pre">genotypes</span> <span class="pre">the</span> <span class="pre">ordering</span> <span class="pre">is</span> <span class="pre">``00``,</span> <span class="pre">``01``,</span> <span class="pre">``11``\n</span>&#160; <span class="pre">(homozygous</span> <span class="pre">reference,</span> <span class="pre">heterozygous,</span> <span class="pre">homozygous</span> <span class="pre">alternate).\n-</span> <span class="pre">For</span> <span class="pre">triallelic,</span> <span class="pre">diploid</span> <span class="pre">genotypes</span> <span class="pre">the</span> <span class="pre">ordering</span> <span class="pre">is</span> <span class="pre">``00``,</span> <span class="pre">``01``,</span> <span class="pre">``11``,\n</span>&#160; <span class="pre">``02``,</span> <span class="pre">``12``,</span> <span class="pre">``22``\n-</span> <span class="pre">For</span> <span class="pre">triallelic,</span> <span class="pre">triploid</span> <span class="pre">genotypes</span> <span class="pre">the</span> <span class="pre">ordering</span> <span class="pre">is</span>&#160; <span class="pre">``000``,</span> <span class="pre">``001``,</span> <span class="pre">``011``,\n</span>&#160; <span class="pre">``111``,</span> <span class="pre">``002``,</span> <span class="pre">``012``,</span> <span class="pre">``112``,</span> <span class="pre">``022``,</span> <span class="pre">``122``,</span> <span class="pre">``222``\n',</span> <span class="pre">kind={'u',</span> <span class="pre">'i'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('variants',</span> <span class="pre">'genotypes'))</span></em><a class="headerlink" href="#sgkit.variables.variant_genotype_count_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_genotype_count_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='variant_genotype_count',</span> <span class="pre">__doc__='\nThe</span> <span class="pre">number</span> <span class="pre">of</span> <span class="pre">observations</span> <span class="pre">for</span> <span class="pre">each</span> <span class="pre">possible</span> <span class="pre">genotype</span> <span class="pre">at</span> <span class="pre">each</span> <span class="pre">variant.\nCounts</span> <span class="pre">are</span> <span class="pre">sorted</span> <span class="pre">following</span> <span class="pre">the</span> <span class="pre">ordering</span> <span class="pre">defined</span> <span class="pre">in</span> <span class="pre">the</span> <span class="pre">VCF</span> <span class="pre">specification.\n\n-</span> <span class="pre">For</span> <span class="pre">biallelic,</span> <span class="pre">diploid</span> <span class="pre">genotypes</span> <span class="pre">the</span> <span class="pre">ordering</span> <span class="pre">is</span> <span class="pre">``00``,</span> <span class="pre">``01``,</span> <span class="pre">``11``\n</span>&#160; <span class="pre">(homozygous</span> <span class="pre">reference,</span> <span class="pre">heterozygous,</span> <span class="pre">homozygous</span> <span class="pre">alternate).\n-</span> <span class="pre">For</span> <span class="pre">triallelic,</span> <span class="pre">diploid</span> <span class="pre">genotypes</span> <span class="pre">the</span> <span class="pre">ordering</span> <span class="pre">is</span> <span class="pre">``00``,</span> <span class="pre">``01``,</span> <span class="pre">``11``,\n</span>&#160; <span class="pre">``02``,</span> <span class="pre">``12``,</span> <span class="pre">``22``\n-</span> <span class="pre">For</span> <span class="pre">triallelic,</span> <span class="pre">triploid</span> <span class="pre">genotypes</span> <span class="pre">the</span> <span class="pre">ordering</span> <span class="pre">is</span>&#160; <span class="pre">``000``,</span> <span class="pre">``001``,</span> <span class="pre">``011``,\n</span>&#160; <span class="pre">``111``,</span> <span class="pre">``002``,</span> <span class="pre">``012``,</span> <span class="pre">``112``,</span> <span class="pre">``022``,</span> <span class="pre">``122``,</span> <span class="pre">``222``\n',</span> <span class="pre">kind={'i',</span> <span class="pre">'u'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('variants',</span> <span class="pre">'genotypes'))</span></em><a class="headerlink" href="#sgkit.variables.variant_genotype_count_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>The number of observations for each possible genotype at each variant.
 Counts are sorted following the ordering defined in the VCF specification.</p>
 <ul class="simple">
diff --git a/latest/generated/sgkit.variables.variant_id_spec.html b/latest/generated/sgkit.variables.variant_id_spec.html
index de979dc49..ffe976cfe 100644
--- a/latest/generated/sgkit.variables.variant_id_spec.html
+++ b/latest/generated/sgkit.variables.variant_id_spec.html
@@ -748,7 +748,7 @@
 <h1>sgkit.variables.variant_id_spec<a class="headerlink" href="#sgkit-variables-variant-id-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.variant_id_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='variant_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">variant.',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('variants',))</span></em><a class="headerlink" href="#sgkit.variables.variant_id_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_id_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='variant_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">variant.',</span> <span class="pre">kind={'U',</span> <span class="pre">'S',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('variants',))</span></em><a class="headerlink" href="#sgkit.variables.variant_id_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>The unique identifier of the variant.</p>
 </dd></dl>
 
diff --git a/latest/searchindex.js b/latest/searchindex.js
index cd22ae407..95f788a17 100644
--- a/latest/searchindex.js
+++ b/latest/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["about", "api", "changelog", "contributing", "examples/gwas_tutorial", "examples/index", "examples/relatedness_tutorial", "generated/sgkit.Fst", "generated/sgkit.Garud_H", "generated/sgkit.Tajimas_D", "generated/sgkit.Weir_Goudet_beta", "generated/sgkit.call_allele_frequencies", "generated/sgkit.cohort_allele_frequencies", "generated/sgkit.convert_call_to_index", "generated/sgkit.convert_probability_to_call", "generated/sgkit.count_call_alleles", "generated/sgkit.count_cohort_alleles", "generated/sgkit.count_variant_alleles", "generated/sgkit.count_variant_genotypes", "generated/sgkit.display_genotypes", "generated/sgkit.display_pedigree", "generated/sgkit.divergence", "generated/sgkit.diversity", "generated/sgkit.filter_partial_calls", "generated/sgkit.genee", "generated/sgkit.genomic_relationship", "generated/sgkit.gwas_linear_regression", "generated/sgkit.hardy_weinberg_test", "generated/sgkit.hybrid_inverse_relationship", "generated/sgkit.hybrid_relationship", "generated/sgkit.identity_by_state", "generated/sgkit.individual_heterozygosity", "generated/sgkit.infer_call_ploidy", "generated/sgkit.infer_sample_ploidy", "generated/sgkit.infer_variant_ploidy", "generated/sgkit.invert_relationship_matrix", "generated/sgkit.io.bgen.bgen_to_zarr", "generated/sgkit.io.bgen.read_bgen", "generated/sgkit.io.bgen.rechunk_bgen", "generated/sgkit.io.plink.plink_to_zarr", "generated/sgkit.io.plink.read_plink", "generated/sgkit.io.plink.write_plink", "generated/sgkit.io.plink.zarr_to_plink", "generated/sgkit.io.vcf.concat_zarrs", "generated/sgkit.io.vcf.partition_into_regions", "generated/sgkit.io.vcf.read_vcf", "generated/sgkit.io.vcf.vcf_to_zarr", "generated/sgkit.io.vcf.vcf_to_zarrs", "generated/sgkit.io.vcf.write_vcf", "generated/sgkit.io.vcf.zarr_array_sizes", "generated/sgkit.io.vcf.zarr_to_vcf", "generated/sgkit.ld_matrix", "generated/sgkit.ld_prune", "generated/sgkit.load_dataset", "generated/sgkit.maximal_independent_set", "generated/sgkit.observed_heterozygosity", "generated/sgkit.pairwise_distance", "generated/sgkit.parent_indices", "generated/sgkit.pbs", "generated/sgkit.pc_relate", "generated/sgkit.pedigree_contribution", "generated/sgkit.pedigree_inbreeding", "generated/sgkit.pedigree_inverse_kinship", "generated/sgkit.pedigree_kinship", "generated/sgkit.pedigree_sel", "generated/sgkit.read_scikit_allel_vcfzarr", "generated/sgkit.regenie", "generated/sgkit.sample_stats", "generated/sgkit.save_dataset", "generated/sgkit.simulate_genedrop", "generated/sgkit.simulate_genotype_call_dataset", "generated/sgkit.variables.call_allele_count_spec", "generated/sgkit.variables.call_allele_frequency_spec", "generated/sgkit.variables.call_dosage_mask_spec", "generated/sgkit.variables.call_dosage_spec", "generated/sgkit.variables.call_genotype_complete_mask_spec", "generated/sgkit.variables.call_genotype_complete_spec", "generated/sgkit.variables.call_genotype_fill_spec", "generated/sgkit.variables.call_genotype_index_mask_spec", "generated/sgkit.variables.call_genotype_index_spec", "generated/sgkit.variables.call_genotype_mask_spec", "generated/sgkit.variables.call_genotype_phased_spec", "generated/sgkit.variables.call_genotype_probability_mask_spec", "generated/sgkit.variables.call_genotype_probability_spec", "generated/sgkit.variables.call_genotype_spec", "generated/sgkit.variables.call_heterozygosity_spec", "generated/sgkit.variables.call_ploidy_spec", "generated/sgkit.variables.cohort_allele_count_spec", "generated/sgkit.variables.cohort_allele_frequency_spec", "generated/sgkit.variables.covariates_spec", "generated/sgkit.variables.interval_contig_name_spec", "generated/sgkit.variables.interval_start_spec", "generated/sgkit.variables.interval_stop_spec", "generated/sgkit.variables.ld_prune_index_to_drop_spec", "generated/sgkit.variables.parent_id_spec", "generated/sgkit.variables.parent_spec", "generated/sgkit.variables.pc_relate_phi_spec", "generated/sgkit.variables.regenie_base_prediction_spec", "generated/sgkit.variables.regenie_loco_prediction_spec", "generated/sgkit.variables.regenie_meta_prediction_spec", "generated/sgkit.variables.sample_call_rate_spec", "generated/sgkit.variables.sample_cohort_spec", "generated/sgkit.variables.sample_id_spec", "generated/sgkit.variables.sample_n_called_spec", "generated/sgkit.variables.sample_n_het_spec", "generated/sgkit.variables.sample_n_hom_alt_spec", "generated/sgkit.variables.sample_n_hom_ref_spec", "generated/sgkit.variables.sample_n_non_ref_spec", "generated/sgkit.variables.sample_pca_component_spec", "generated/sgkit.variables.sample_pca_explained_variance_ratio_spec", "generated/sgkit.variables.sample_pca_explained_variance_spec", "generated/sgkit.variables.sample_pca_loading_spec", "generated/sgkit.variables.sample_pca_projection_spec", "generated/sgkit.variables.sample_ploidy_spec", "generated/sgkit.variables.stat_Fst_spec", "generated/sgkit.variables.stat_Garud_h123_spec", "generated/sgkit.variables.stat_Garud_h12_spec", "generated/sgkit.variables.stat_Garud_h1_spec", "generated/sgkit.variables.stat_Garud_h2_h1_spec", "generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec", "generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec", "generated/sgkit.variables.stat_Tajimas_D_spec", "generated/sgkit.variables.stat_Weir_Goudet_beta_spec", "generated/sgkit.variables.stat_divergence_spec", "generated/sgkit.variables.stat_diversity_spec", "generated/sgkit.variables.stat_genomic_kinship_spec", "generated/sgkit.variables.stat_genomic_relationship_spec", "generated/sgkit.variables.stat_hybrid_inverse_relationship_spec", "generated/sgkit.variables.stat_hybrid_relationship_spec", "generated/sgkit.variables.stat_identity_by_state_spec", "generated/sgkit.variables.stat_inverse_relationship_spec", "generated/sgkit.variables.stat_observed_heterozygosity_spec", "generated/sgkit.variables.stat_pbs_spec", "generated/sgkit.variables.stat_pedigree_contribution_spec", "generated/sgkit.variables.stat_pedigree_inbreeding_spec", "generated/sgkit.variables.stat_pedigree_inverse_kinship_spec", "generated/sgkit.variables.stat_pedigree_inverse_relationship_spec", "generated/sgkit.variables.stat_pedigree_kinship_spec", "generated/sgkit.variables.stat_pedigree_relationship_spec", "generated/sgkit.variables.traits_spec", "generated/sgkit.variables.variant_allele_count_spec", "generated/sgkit.variables.variant_allele_frequency_spec", "generated/sgkit.variables.variant_allele_spec", "generated/sgkit.variables.variant_allele_total_spec", "generated/sgkit.variables.variant_call_rate_spec", "generated/sgkit.variables.variant_contig_spec", "generated/sgkit.variables.variant_genotype_count_spec", "generated/sgkit.variables.variant_hwe_p_value_spec", "generated/sgkit.variables.variant_id_spec", "generated/sgkit.variables.variant_linreg_beta_spec", "generated/sgkit.variables.variant_linreg_p_value_spec", "generated/sgkit.variables.variant_linreg_t_value_spec", "generated/sgkit.variables.variant_n_called_spec", "generated/sgkit.variables.variant_n_het_spec", "generated/sgkit.variables.variant_n_hom_alt_spec", "generated/sgkit.variables.variant_n_hom_ref_spec", "generated/sgkit.variables.variant_n_non_ref_spec", "generated/sgkit.variables.variant_ploidy_spec", "generated/sgkit.variables.variant_position_spec", "generated/sgkit.variables.variant_score_spec", "generated/sgkit.variables.window_contig_spec", "generated/sgkit.variables.window_start_spec", "generated/sgkit.variables.window_stop_spec", "generated/sgkit.variant_stats", "generated/sgkit.window_by_genome", "generated/sgkit.window_by_interval", "generated/sgkit.window_by_position", "generated/sgkit.window_by_variant", "getting_started", "how_do_i", "index", "news", "news/introducing_sgkit", "user_guide", "vcf"], "filenames": ["about.rst", "api.rst", "changelog.rst", "contributing.rst", "examples/gwas_tutorial.ipynb", "examples/index.rst", "examples/relatedness_tutorial.ipynb", "generated/sgkit.Fst.rst", "generated/sgkit.Garud_H.rst", "generated/sgkit.Tajimas_D.rst", "generated/sgkit.Weir_Goudet_beta.rst", "generated/sgkit.call_allele_frequencies.rst", "generated/sgkit.cohort_allele_frequencies.rst", "generated/sgkit.convert_call_to_index.rst", "generated/sgkit.convert_probability_to_call.rst", "generated/sgkit.count_call_alleles.rst", "generated/sgkit.count_cohort_alleles.rst", "generated/sgkit.count_variant_alleles.rst", "generated/sgkit.count_variant_genotypes.rst", "generated/sgkit.display_genotypes.rst", "generated/sgkit.display_pedigree.rst", "generated/sgkit.divergence.rst", "generated/sgkit.diversity.rst", "generated/sgkit.filter_partial_calls.rst", "generated/sgkit.genee.rst", "generated/sgkit.genomic_relationship.rst", "generated/sgkit.gwas_linear_regression.rst", "generated/sgkit.hardy_weinberg_test.rst", "generated/sgkit.hybrid_inverse_relationship.rst", "generated/sgkit.hybrid_relationship.rst", "generated/sgkit.identity_by_state.rst", "generated/sgkit.individual_heterozygosity.rst", "generated/sgkit.infer_call_ploidy.rst", "generated/sgkit.infer_sample_ploidy.rst", "generated/sgkit.infer_variant_ploidy.rst", "generated/sgkit.invert_relationship_matrix.rst", "generated/sgkit.io.bgen.bgen_to_zarr.rst", "generated/sgkit.io.bgen.read_bgen.rst", "generated/sgkit.io.bgen.rechunk_bgen.rst", "generated/sgkit.io.plink.plink_to_zarr.rst", "generated/sgkit.io.plink.read_plink.rst", "generated/sgkit.io.plink.write_plink.rst", "generated/sgkit.io.plink.zarr_to_plink.rst", "generated/sgkit.io.vcf.concat_zarrs.rst", "generated/sgkit.io.vcf.partition_into_regions.rst", "generated/sgkit.io.vcf.read_vcf.rst", "generated/sgkit.io.vcf.vcf_to_zarr.rst", "generated/sgkit.io.vcf.vcf_to_zarrs.rst", "generated/sgkit.io.vcf.write_vcf.rst", "generated/sgkit.io.vcf.zarr_array_sizes.rst", "generated/sgkit.io.vcf.zarr_to_vcf.rst", "generated/sgkit.ld_matrix.rst", "generated/sgkit.ld_prune.rst", "generated/sgkit.load_dataset.rst", "generated/sgkit.maximal_independent_set.rst", "generated/sgkit.observed_heterozygosity.rst", "generated/sgkit.pairwise_distance.rst", "generated/sgkit.parent_indices.rst", "generated/sgkit.pbs.rst", "generated/sgkit.pc_relate.rst", "generated/sgkit.pedigree_contribution.rst", "generated/sgkit.pedigree_inbreeding.rst", "generated/sgkit.pedigree_inverse_kinship.rst", "generated/sgkit.pedigree_kinship.rst", "generated/sgkit.pedigree_sel.rst", "generated/sgkit.read_scikit_allel_vcfzarr.rst", "generated/sgkit.regenie.rst", "generated/sgkit.sample_stats.rst", "generated/sgkit.save_dataset.rst", "generated/sgkit.simulate_genedrop.rst", "generated/sgkit.simulate_genotype_call_dataset.rst", "generated/sgkit.variables.call_allele_count_spec.rst", "generated/sgkit.variables.call_allele_frequency_spec.rst", "generated/sgkit.variables.call_dosage_mask_spec.rst", "generated/sgkit.variables.call_dosage_spec.rst", "generated/sgkit.variables.call_genotype_complete_mask_spec.rst", "generated/sgkit.variables.call_genotype_complete_spec.rst", "generated/sgkit.variables.call_genotype_fill_spec.rst", "generated/sgkit.variables.call_genotype_index_mask_spec.rst", "generated/sgkit.variables.call_genotype_index_spec.rst", "generated/sgkit.variables.call_genotype_mask_spec.rst", "generated/sgkit.variables.call_genotype_phased_spec.rst", "generated/sgkit.variables.call_genotype_probability_mask_spec.rst", "generated/sgkit.variables.call_genotype_probability_spec.rst", "generated/sgkit.variables.call_genotype_spec.rst", "generated/sgkit.variables.call_heterozygosity_spec.rst", "generated/sgkit.variables.call_ploidy_spec.rst", "generated/sgkit.variables.cohort_allele_count_spec.rst", "generated/sgkit.variables.cohort_allele_frequency_spec.rst", "generated/sgkit.variables.covariates_spec.rst", "generated/sgkit.variables.interval_contig_name_spec.rst", "generated/sgkit.variables.interval_start_spec.rst", "generated/sgkit.variables.interval_stop_spec.rst", "generated/sgkit.variables.ld_prune_index_to_drop_spec.rst", "generated/sgkit.variables.parent_id_spec.rst", "generated/sgkit.variables.parent_spec.rst", "generated/sgkit.variables.pc_relate_phi_spec.rst", "generated/sgkit.variables.regenie_base_prediction_spec.rst", "generated/sgkit.variables.regenie_loco_prediction_spec.rst", "generated/sgkit.variables.regenie_meta_prediction_spec.rst", "generated/sgkit.variables.sample_call_rate_spec.rst", "generated/sgkit.variables.sample_cohort_spec.rst", "generated/sgkit.variables.sample_id_spec.rst", "generated/sgkit.variables.sample_n_called_spec.rst", "generated/sgkit.variables.sample_n_het_spec.rst", "generated/sgkit.variables.sample_n_hom_alt_spec.rst", "generated/sgkit.variables.sample_n_hom_ref_spec.rst", "generated/sgkit.variables.sample_n_non_ref_spec.rst", "generated/sgkit.variables.sample_pca_component_spec.rst", "generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.rst", "generated/sgkit.variables.sample_pca_explained_variance_spec.rst", "generated/sgkit.variables.sample_pca_loading_spec.rst", "generated/sgkit.variables.sample_pca_projection_spec.rst", "generated/sgkit.variables.sample_ploidy_spec.rst", "generated/sgkit.variables.stat_Fst_spec.rst", "generated/sgkit.variables.stat_Garud_h123_spec.rst", "generated/sgkit.variables.stat_Garud_h12_spec.rst", "generated/sgkit.variables.stat_Garud_h1_spec.rst", "generated/sgkit.variables.stat_Garud_h2_h1_spec.rst", "generated/sgkit.variables.stat_Hamilton_Kerr_lambda_spec.rst", "generated/sgkit.variables.stat_Hamilton_Kerr_tau_spec.rst", "generated/sgkit.variables.stat_Tajimas_D_spec.rst", "generated/sgkit.variables.stat_Weir_Goudet_beta_spec.rst", "generated/sgkit.variables.stat_divergence_spec.rst", "generated/sgkit.variables.stat_diversity_spec.rst", "generated/sgkit.variables.stat_genomic_kinship_spec.rst", "generated/sgkit.variables.stat_genomic_relationship_spec.rst", "generated/sgkit.variables.stat_hybrid_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_hybrid_relationship_spec.rst", "generated/sgkit.variables.stat_identity_by_state_spec.rst", "generated/sgkit.variables.stat_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_observed_heterozygosity_spec.rst", "generated/sgkit.variables.stat_pbs_spec.rst", "generated/sgkit.variables.stat_pedigree_contribution_spec.rst", "generated/sgkit.variables.stat_pedigree_inbreeding_spec.rst", "generated/sgkit.variables.stat_pedigree_inverse_kinship_spec.rst", "generated/sgkit.variables.stat_pedigree_inverse_relationship_spec.rst", "generated/sgkit.variables.stat_pedigree_kinship_spec.rst", "generated/sgkit.variables.stat_pedigree_relationship_spec.rst", "generated/sgkit.variables.traits_spec.rst", "generated/sgkit.variables.variant_allele_count_spec.rst", "generated/sgkit.variables.variant_allele_frequency_spec.rst", "generated/sgkit.variables.variant_allele_spec.rst", "generated/sgkit.variables.variant_allele_total_spec.rst", "generated/sgkit.variables.variant_call_rate_spec.rst", "generated/sgkit.variables.variant_contig_spec.rst", "generated/sgkit.variables.variant_genotype_count_spec.rst", "generated/sgkit.variables.variant_hwe_p_value_spec.rst", "generated/sgkit.variables.variant_id_spec.rst", "generated/sgkit.variables.variant_linreg_beta_spec.rst", "generated/sgkit.variables.variant_linreg_p_value_spec.rst", "generated/sgkit.variables.variant_linreg_t_value_spec.rst", "generated/sgkit.variables.variant_n_called_spec.rst", "generated/sgkit.variables.variant_n_het_spec.rst", "generated/sgkit.variables.variant_n_hom_alt_spec.rst", "generated/sgkit.variables.variant_n_hom_ref_spec.rst", "generated/sgkit.variables.variant_n_non_ref_spec.rst", "generated/sgkit.variables.variant_ploidy_spec.rst", "generated/sgkit.variables.variant_position_spec.rst", "generated/sgkit.variables.variant_score_spec.rst", "generated/sgkit.variables.window_contig_spec.rst", "generated/sgkit.variables.window_start_spec.rst", "generated/sgkit.variables.window_stop_spec.rst", "generated/sgkit.variant_stats.rst", "generated/sgkit.window_by_genome.rst", "generated/sgkit.window_by_interval.rst", "generated/sgkit.window_by_position.rst", "generated/sgkit.window_by_variant.rst", "getting_started.rst", "how_do_i.rst", "index.rst", "news.rst", "news/introducing_sgkit.md", "user_guide.rst", "vcf.rst"], "titles": ["About", "API reference", "Changelog", "Contributing to sgkit", "GWAS Tutorial", "Examples", "Relatedness Tutorial", "sgkit.Fst", "sgkit.Garud_H", "sgkit.Tajimas_D", "sgkit.Weir_Goudet_beta", "sgkit.call_allele_frequencies", "sgkit.cohort_allele_frequencies", "sgkit.convert_call_to_index", "sgkit.convert_probability_to_call", "sgkit.count_call_alleles", "sgkit.count_cohort_alleles", "sgkit.count_variant_alleles", "sgkit.count_variant_genotypes", "sgkit.display_genotypes", "sgkit.display_pedigree", "sgkit.divergence", "sgkit.diversity", "sgkit.filter_partial_calls", "sgkit.genee", "sgkit.genomic_relationship", "sgkit.gwas_linear_regression", "sgkit.hardy_weinberg_test", "sgkit.hybrid_inverse_relationship", "sgkit.hybrid_relationship", "sgkit.identity_by_state", "sgkit.individual_heterozygosity", "sgkit.infer_call_ploidy", "sgkit.infer_sample_ploidy", "sgkit.infer_variant_ploidy", "sgkit.invert_relationship_matrix", "sgkit.io.bgen.bgen_to_zarr", "sgkit.io.bgen.read_bgen", "sgkit.io.bgen.rechunk_bgen", "sgkit.io.plink.plink_to_zarr", "sgkit.io.plink.read_plink", "sgkit.io.plink.write_plink", "sgkit.io.plink.zarr_to_plink", "sgkit.io.vcf.concat_zarrs", "sgkit.io.vcf.partition_into_regions", "sgkit.io.vcf.read_vcf", "sgkit.io.vcf.vcf_to_zarr", "sgkit.io.vcf.vcf_to_zarrs", "sgkit.io.vcf.write_vcf", "sgkit.io.vcf.zarr_array_sizes", "sgkit.io.vcf.zarr_to_vcf", "sgkit.ld_matrix", "sgkit.ld_prune", "sgkit.load_dataset", "sgkit.maximal_independent_set", "sgkit.observed_heterozygosity", "sgkit.pairwise_distance", "sgkit.parent_indices", "sgkit.pbs", "sgkit.pc_relate", "sgkit.pedigree_contribution", "sgkit.pedigree_inbreeding", "sgkit.pedigree_inverse_kinship", "sgkit.pedigree_kinship", "sgkit.pedigree_sel", "sgkit.read_scikit_allel_vcfzarr", "sgkit.regenie", "sgkit.sample_stats", "sgkit.save_dataset", "sgkit.simulate_genedrop", "sgkit.simulate_genotype_call_dataset", "sgkit.variables.call_allele_count_spec", "sgkit.variables.call_allele_frequency_spec", "sgkit.variables.call_dosage_mask_spec", "sgkit.variables.call_dosage_spec", "sgkit.variables.call_genotype_complete_mask_spec", "sgkit.variables.call_genotype_complete_spec", "sgkit.variables.call_genotype_fill_spec", "sgkit.variables.call_genotype_index_mask_spec", "sgkit.variables.call_genotype_index_spec", "sgkit.variables.call_genotype_mask_spec", "sgkit.variables.call_genotype_phased_spec", "sgkit.variables.call_genotype_probability_mask_spec", 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[173, "bgen"]], "PLINK": [[1, "plink"], [173, "plink"]], "VCF (reading)": [[1, "vcf-reading"]], "VCF (writing)": [[1, "vcf-writing"]], "Dataset": [[1, "dataset"]], "Methods": [[1, "methods"], [173, "methods"]], "Basic genetics statistics": [[1, "basic-genetics-statistics"]], "Population genetic statistics": [[1, "population-genetic-statistics"]], "Relatedness": [[1, "relatedness"]], "Linkage Disequilibrium": [[1, "linkage-disequilibrium"]], "Genetic Association and Regression": [[1, "genetic-association-and-regression"]], "Miscellaneous": [[1, "miscellaneous"]], "Utilities": [[1, "utilities"]], "Variables": [[1, "variables"]], "Changelog": [[2, "changelog"]], "0.10.0 (unreleased)": [[2, "unreleased"]], "New Features": [[2, "new-features"], [2, "id1"], [2, "id3"], [2, "id7"]], "0.9.0 (24 June 2024)": [[2, "june-2024"]], "Deprecations": [[2, "deprecations"], [2, "id4"]], "Improvements": [[2, "improvements"], [2, "id2"], [2, "id5"], [2, "id9"]], "0.8.0 (1 May 2024)": [[2, "may-2024"]], "Bug fixes": [[2, "bug-fixes"], [2, "id6"], [2, "id10"]], "Documentation": [[2, "documentation"]], "0.7.0 (2 May 2023)": [[2, "may-2023"]], "Breaking changes": [[2, "breaking-changes"], [2, "id8"]], "0.6.0 (1 February 2023)": [[2, "february-2023"]], "Contributing to sgkit": [[3, "contributing-to-sgkit"]], "Table of contents:": [[3, "table-of-contents"], [168, "table-of-contents"], [173, "table-of-contents"], [174, "table-of-contents"]], "Discussion forums": [[3, "discussion-forums"]], "Code repositories": [[3, "code-repositories"]], "Issues": [[3, "issues"]], "Development environment": [[3, "development-environment"]], "Download code": [[3, "download-code"]], "Install": [[3, "install"]], "Run tests": [[3, "run-tests"]], "Contributing to code": [[3, "contributing-to-code"]], "Continuous Integration": [[3, "continuous-integration"]], "Test": [[3, "test"]], "Docstrings": [[3, "docstrings"]], "Coding standards": [[3, "coding-standards"]], "PR/Git ops": [[3, "pr-git-ops"]], "Python dependencies": [[3, "python-dependencies"]], "Contributing to documentation": [[3, "contributing-to-documentation"]], "Benchmarks": [[3, "benchmarks"]], "Review process": [[3, "review-process"]], "Design discussions": [[3, "design-discussions"]], "Dataset subclassing": [[3, "dataset-subclassing"]], "Dataset API typing": [[3, "dataset-api-typing"]], "Dataset variables": [[3, "dataset-variables"]], "Delayed invariant checks": [[3, "delayed-invariant-checks"]], "Mixed ploidy": [[3, "mixed-ploidy"]], "Numba guvectorize usage": [[3, "numba-guvectorize-usage"]], "API namespace": [[3, "api-namespace"]], "GWAS Tutorial": [[4, "gwas-tutorial"]], "Download public 1000 Genomes data": [[4, "download-public-1000-genomes-data"]], "Importing data from VCF": [[4, "importing-data-from-vcf"]], "Getting to know our data": [[4, "getting-to-know-our-data"]], "Adding column fields": [[4, "adding-column-fields"]], "Query functions": [[4, "query-functions"]], "Quality control": [[4, "quality-control"]], "Let\u2019s do a GWAS!": [[4, "let-s-do-a-gwas"]], "Confounded!": [[4, "confounded"]], "Examples": [[5, "examples"]], "Relatedness Tutorial": [[6, "relatedness-tutorial"]], "Download the pig dataset": [[6, "download-the-pig-dataset"]], "Reading pedigree data": [[6, "reading-pedigree-data"]], "Working with pedigree data": [[6, "working-with-pedigree-data"]], "Pedigree relationships": [[6, "pedigree-relationships"]], "Genomic relationships": [[6, "genomic-relationships"]], "The VanRaden GRM": [[6, "the-vanraden-grm"]], "A better estimate of ancestral allele frequencies": [[6, "a-better-estimate-of-ancestral-allele-frequencies"]], "Weir-Goudet GRM": [[6, "weir-goudet-grm"]], "Hybrid relationship matrices": [[6, "hybrid-relationship-matrices"]], "References": [[6, "references"]], "sgkit.Fst": [[7, "sgkit-fst"]], "sgkit.Garud_H": [[8, "sgkit-garud-h"]], "sgkit.Tajimas_D": [[9, "sgkit-tajimas-d"]], "sgkit.Weir_Goudet_beta": [[10, "sgkit-weir-goudet-beta"]], "sgkit.call_allele_frequencies": [[11, "sgkit-call-allele-frequencies"]], "sgkit.cohort_allele_frequencies": [[12, "sgkit-cohort-allele-frequencies"]], "sgkit.convert_call_to_index": [[13, "sgkit-convert-call-to-index"]], "sgkit.convert_probability_to_call": [[14, "sgkit-convert-probability-to-call"]], "sgkit.count_call_alleles": [[15, "sgkit-count-call-alleles"]], "sgkit.count_cohort_alleles": [[16, "sgkit-count-cohort-alleles"]], "sgkit.count_variant_alleles": [[17, "sgkit-count-variant-alleles"]], "sgkit.count_variant_genotypes": [[18, "sgkit-count-variant-genotypes"]], "sgkit.display_genotypes": [[19, "sgkit-display-genotypes"]], "sgkit.display_pedigree": [[20, "sgkit-display-pedigree"]], "sgkit.divergence": [[21, "sgkit-divergence"]], "sgkit.diversity": [[22, "sgkit-diversity"]], "sgkit.filter_partial_calls": [[23, "sgkit-filter-partial-calls"]], "sgkit.genee": [[24, "sgkit-genee"]], "sgkit.genomic_relationship": [[25, "sgkit-genomic-relationship"]], "sgkit.gwas_linear_regression": [[26, "sgkit-gwas-linear-regression"]], "sgkit.hardy_weinberg_test": [[27, "sgkit-hardy-weinberg-test"]], "sgkit.hybrid_inverse_relationship": [[28, "sgkit-hybrid-inverse-relationship"]], "sgkit.hybrid_relationship": [[29, "sgkit-hybrid-relationship"]], "sgkit.identity_by_state": [[30, "sgkit-identity-by-state"]], "sgkit.individual_heterozygosity": [[31, "sgkit-individual-heterozygosity"]], "sgkit.infer_call_ploidy": [[32, "sgkit-infer-call-ploidy"]], "sgkit.infer_sample_ploidy": [[33, "sgkit-infer-sample-ploidy"]], "sgkit.infer_variant_ploidy": [[34, "sgkit-infer-variant-ploidy"]], "sgkit.invert_relationship_matrix": [[35, "sgkit-invert-relationship-matrix"]], "sgkit.io.bgen.bgen_to_zarr": [[36, "sgkit-io-bgen-bgen-to-zarr"]], "sgkit.io.bgen.read_bgen": [[37, "sgkit-io-bgen-read-bgen"]], "sgkit.io.bgen.rechunk_bgen": [[38, "sgkit-io-bgen-rechunk-bgen"]], "sgkit.io.plink.plink_to_zarr": [[39, "sgkit-io-plink-plink-to-zarr"]], "sgkit.io.plink.read_plink": [[40, "sgkit-io-plink-read-plink"]], "sgkit.io.plink.write_plink": [[41, "sgkit-io-plink-write-plink"]], "sgkit.io.plink.zarr_to_plink": [[42, "sgkit-io-plink-zarr-to-plink"]], "sgkit.io.vcf.concat_zarrs": [[43, "sgkit-io-vcf-concat-zarrs"]], "sgkit.io.vcf.partition_into_regions": [[44, "sgkit-io-vcf-partition-into-regions"]], "sgkit.io.vcf.read_vcf": [[45, "sgkit-io-vcf-read-vcf"]], "sgkit.io.vcf.vcf_to_zarr": [[46, "sgkit-io-vcf-vcf-to-zarr"]], "sgkit.io.vcf.vcf_to_zarrs": [[47, "sgkit-io-vcf-vcf-to-zarrs"]], "sgkit.io.vcf.write_vcf": [[48, "sgkit-io-vcf-write-vcf"]], "sgkit.io.vcf.zarr_array_sizes": [[49, "sgkit-io-vcf-zarr-array-sizes"]], "sgkit.io.vcf.zarr_to_vcf": [[50, "sgkit-io-vcf-zarr-to-vcf"]], "sgkit.ld_matrix": [[51, "sgkit-ld-matrix"]], "sgkit.ld_prune": [[52, "sgkit-ld-prune"]], "sgkit.load_dataset": [[53, "sgkit-load-dataset"]], "sgkit.maximal_independent_set": [[54, "sgkit-maximal-independent-set"]], "sgkit.observed_heterozygosity": [[55, "sgkit-observed-heterozygosity"]], "sgkit.pairwise_distance": [[56, "sgkit-pairwise-distance"]], "sgkit.parent_indices": [[57, "sgkit-parent-indices"]], "sgkit.pbs": [[58, "sgkit-pbs"]], "sgkit.pc_relate": [[59, "sgkit-pc-relate"]], "sgkit.pedigree_contribution": [[60, "sgkit-pedigree-contribution"]], "sgkit.pedigree_inbreeding": [[61, "sgkit-pedigree-inbreeding"]], "sgkit.pedigree_inverse_kinship": [[62, "sgkit-pedigree-inverse-kinship"]], "sgkit.pedigree_kinship": [[63, "sgkit-pedigree-kinship"]], "sgkit.pedigree_sel": [[64, "sgkit-pedigree-sel"]], "sgkit.read_scikit_allel_vcfzarr": [[65, "sgkit-read-scikit-allel-vcfzarr"]], "sgkit.regenie": [[66, "sgkit-regenie"]], "sgkit.sample_stats": [[67, "sgkit-sample-stats"]], "sgkit.save_dataset": [[68, "sgkit-save-dataset"]], "sgkit.simulate_genedrop": [[69, "sgkit-simulate-genedrop"]], "sgkit.simulate_genotype_call_dataset": [[70, "sgkit-simulate-genotype-call-dataset"]], "sgkit.variables.call_allele_count_spec": [[71, "sgkit-variables-call-allele-count-spec"]], "sgkit.variables.call_allele_frequency_spec": [[72, "sgkit-variables-call-allele-frequency-spec"]], "sgkit.variables.call_dosage_mask_spec": [[73, "sgkit-variables-call-dosage-mask-spec"]], "sgkit.variables.call_dosage_spec": [[74, "sgkit-variables-call-dosage-spec"]], "sgkit.variables.call_genotype_complete_mask_spec": [[75, "sgkit-variables-call-genotype-complete-mask-spec"]], "sgkit.variables.call_genotype_complete_spec": [[76, "sgkit-variables-call-genotype-complete-spec"]], "sgkit.variables.call_genotype_fill_spec": [[77, "sgkit-variables-call-genotype-fill-spec"]], "sgkit.variables.call_genotype_index_mask_spec": [[78, "sgkit-variables-call-genotype-index-mask-spec"]], "sgkit.variables.call_genotype_index_spec": [[79, "sgkit-variables-call-genotype-index-spec"]], "sgkit.variables.call_genotype_mask_spec": [[80, "sgkit-variables-call-genotype-mask-spec"]], "sgkit.variables.call_genotype_phased_spec": [[81, "sgkit-variables-call-genotype-phased-spec"]], "sgkit.variables.call_genotype_probability_mask_spec": [[82, 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"sgkit.variables.ld_prune_index_to_drop_spec": [[93, "sgkit-variables-ld-prune-index-to-drop-spec"]], "sgkit.variables.parent_id_spec": [[94, "sgkit-variables-parent-id-spec"]], "sgkit.variables.parent_spec": [[95, "sgkit-variables-parent-spec"]], "sgkit.variables.pc_relate_phi_spec": [[96, "sgkit-variables-pc-relate-phi-spec"]], "sgkit.variables.regenie_base_prediction_spec": [[97, "sgkit-variables-regenie-base-prediction-spec"]], "sgkit.variables.regenie_loco_prediction_spec": [[98, "sgkit-variables-regenie-loco-prediction-spec"]], "sgkit.variables.regenie_meta_prediction_spec": [[99, "sgkit-variables-regenie-meta-prediction-spec"]], "sgkit.variables.sample_call_rate_spec": [[100, "sgkit-variables-sample-call-rate-spec"]], "sgkit.variables.sample_cohort_spec": [[101, "sgkit-variables-sample-cohort-spec"]], "sgkit.variables.sample_id_spec": [[102, "sgkit-variables-sample-id-spec"]], "sgkit.variables.sample_n_called_spec": [[103, "sgkit-variables-sample-n-called-spec"]], "sgkit.variables.sample_n_het_spec": [[104, "sgkit-variables-sample-n-het-spec"]], "sgkit.variables.sample_n_hom_alt_spec": [[105, "sgkit-variables-sample-n-hom-alt-spec"]], "sgkit.variables.sample_n_hom_ref_spec": [[106, "sgkit-variables-sample-n-hom-ref-spec"]], "sgkit.variables.sample_n_non_ref_spec": [[107, "sgkit-variables-sample-n-non-ref-spec"]], "sgkit.variables.sample_pca_component_spec": [[108, "sgkit-variables-sample-pca-component-spec"]], "sgkit.variables.sample_pca_explained_variance_ratio_spec": [[109, "sgkit-variables-sample-pca-explained-variance-ratio-spec"]], "sgkit.variables.sample_pca_explained_variance_spec": [[110, "sgkit-variables-sample-pca-explained-variance-spec"]], "sgkit.variables.sample_pca_loading_spec": [[111, "sgkit-variables-sample-pca-loading-spec"]], "sgkit.variables.sample_pca_projection_spec": [[112, "sgkit-variables-sample-pca-projection-spec"]], "sgkit.variables.sample_ploidy_spec": [[113, "sgkit-variables-sample-ploidy-spec"]], "sgkit.variables.stat_Fst_spec": [[114, "sgkit-variables-stat-fst-spec"]], "sgkit.variables.stat_Garud_h123_spec": [[115, "sgkit-variables-stat-garud-h123-spec"]], "sgkit.variables.stat_Garud_h12_spec": [[116, "sgkit-variables-stat-garud-h12-spec"]], "sgkit.variables.stat_Garud_h1_spec": [[117, "sgkit-variables-stat-garud-h1-spec"]], "sgkit.variables.stat_Garud_h2_h1_spec": [[118, "sgkit-variables-stat-garud-h2-h1-spec"]], "sgkit.variables.stat_Hamilton_Kerr_lambda_spec": [[119, "sgkit-variables-stat-hamilton-kerr-lambda-spec"]], "sgkit.variables.stat_Hamilton_Kerr_tau_spec": [[120, "sgkit-variables-stat-hamilton-kerr-tau-spec"]], "sgkit.variables.stat_Tajimas_D_spec": [[121, "sgkit-variables-stat-tajimas-d-spec"]], "sgkit.variables.stat_Weir_Goudet_beta_spec": [[122, "sgkit-variables-stat-weir-goudet-beta-spec"]], "sgkit.variables.stat_divergence_spec": [[123, "sgkit-variables-stat-divergence-spec"]], "sgkit.variables.stat_diversity_spec": [[124, "sgkit-variables-stat-diversity-spec"]], "sgkit.variables.stat_genomic_kinship_spec": [[125, "sgkit-variables-stat-genomic-kinship-spec"]], "sgkit.variables.stat_genomic_relationship_spec": [[126, "sgkit-variables-stat-genomic-relationship-spec"]], "sgkit.variables.stat_hybrid_inverse_relationship_spec": [[127, "sgkit-variables-stat-hybrid-inverse-relationship-spec"]], "sgkit.variables.stat_hybrid_relationship_spec": [[128, "sgkit-variables-stat-hybrid-relationship-spec"]], "sgkit.variables.stat_identity_by_state_spec": [[129, "sgkit-variables-stat-identity-by-state-spec"]], "sgkit.variables.stat_inverse_relationship_spec": [[130, "sgkit-variables-stat-inverse-relationship-spec"]], "sgkit.variables.stat_observed_heterozygosity_spec": [[131, "sgkit-variables-stat-observed-heterozygosity-spec"]], "sgkit.variables.stat_pbs_spec": [[132, "sgkit-variables-stat-pbs-spec"]], "sgkit.variables.stat_pedigree_contribution_spec": [[133, "sgkit-variables-stat-pedigree-contribution-spec"]], "sgkit.variables.stat_pedigree_inbreeding_spec": [[134, "sgkit-variables-stat-pedigree-inbreeding-spec"]], "sgkit.variables.stat_pedigree_inverse_kinship_spec": [[135, "sgkit-variables-stat-pedigree-inverse-kinship-spec"]], "sgkit.variables.stat_pedigree_inverse_relationship_spec": [[136, "sgkit-variables-stat-pedigree-inverse-relationship-spec"]], "sgkit.variables.stat_pedigree_kinship_spec": [[137, "sgkit-variables-stat-pedigree-kinship-spec"]], "sgkit.variables.stat_pedigree_relationship_spec": [[138, "sgkit-variables-stat-pedigree-relationship-spec"]], "sgkit.variables.traits_spec": [[139, "sgkit-variables-traits-spec"]], "sgkit.variables.variant_allele_count_spec": [[140, "sgkit-variables-variant-allele-count-spec"]], "sgkit.variables.variant_allele_frequency_spec": [[141, "sgkit-variables-variant-allele-frequency-spec"]], "sgkit.variables.variant_allele_spec": [[142, "sgkit-variables-variant-allele-spec"]], "sgkit.variables.variant_allele_total_spec": [[143, "sgkit-variables-variant-allele-total-spec"]], "sgkit.variables.variant_call_rate_spec": [[144, "sgkit-variables-variant-call-rate-spec"]], "sgkit.variables.variant_contig_spec": [[145, "sgkit-variables-variant-contig-spec"]], "sgkit.variables.variant_genotype_count_spec": [[146, "sgkit-variables-variant-genotype-count-spec"]], "sgkit.variables.variant_hwe_p_value_spec": [[147, "sgkit-variables-variant-hwe-p-value-spec"]], "sgkit.variables.variant_id_spec": [[148, "sgkit-variables-variant-id-spec"]], "sgkit.variables.variant_linreg_beta_spec": [[149, "sgkit-variables-variant-linreg-beta-spec"]], "sgkit.variables.variant_linreg_p_value_spec": [[150, "sgkit-variables-variant-linreg-p-value-spec"]], "sgkit.variables.variant_linreg_t_value_spec": [[151, "sgkit-variables-variant-linreg-t-value-spec"]], "sgkit.variables.variant_n_called_spec": [[152, "sgkit-variables-variant-n-called-spec"]], "sgkit.variables.variant_n_het_spec": [[153, "sgkit-variables-variant-n-het-spec"]], "sgkit.variables.variant_n_hom_alt_spec": [[154, "sgkit-variables-variant-n-hom-alt-spec"]], "sgkit.variables.variant_n_hom_ref_spec": [[155, "sgkit-variables-variant-n-hom-ref-spec"]], "sgkit.variables.variant_n_non_ref_spec": [[156, "sgkit-variables-variant-n-non-ref-spec"]], "sgkit.variables.variant_ploidy_spec": [[157, "sgkit-variables-variant-ploidy-spec"]], "sgkit.variables.variant_position_spec": [[158, "sgkit-variables-variant-position-spec"]], "sgkit.variables.variant_score_spec": [[159, "sgkit-variables-variant-score-spec"]], "sgkit.variables.window_contig_spec": [[160, "sgkit-variables-window-contig-spec"]], "sgkit.variables.window_start_spec": [[161, "sgkit-variables-window-start-spec"]], "sgkit.variables.window_stop_spec": [[162, "sgkit-variables-window-stop-spec"]], "sgkit.variant_stats": [[163, "sgkit-variant-stats"]], "sgkit.window_by_genome": [[164, "sgkit-window-by-genome"]], "sgkit.window_by_interval": [[165, "sgkit-window-by-interval"]], "sgkit.window_by_position": [[166, "sgkit-window-by-position"]], "sgkit.window_by_variant": [[167, "sgkit-window-by-variant"]], "Getting Started": [[168, "getting-started"]], "Installation": [[168, "installation"], [173, "installation"], [174, "installation"]], "Overview": [[168, "overview"]], "Data structures": [[168, "data-structures"]], "Genetic methods": [[168, "genetic-methods"]], "Missing data": [[168, "missing-data"]], "Windowing": [[168, "windowing"]], "Cohorts": [[168, "cohorts"]], "Chaining operations": [[168, "chaining-operations"]], "Chunked arrays": [[168, "chunked-arrays"]], "How do I \u2026": [[169, "how-do-i"]], "Create a test dataset?": [[169, "create-a-test-dataset"]], "Look at the dataset summary?": [[169, "look-at-the-dataset-summary"]], "Get the values for a variable in a dataset?": [[169, "get-the-values-for-a-variable-in-a-dataset"]], "Find the definition for a variable in a dataset?": [[169, "find-the-definition-for-a-variable-in-a-dataset"]], "Look at the genotypes?": [[169, "look-at-the-genotypes"]], "Subset the variables?": [[169, "subset-the-variables"]], "Subset to a genomic range?": [[169, "subset-to-a-genomic-range"]], "Get the list of samples?": [[169, "get-the-list-of-samples"]], "Subset the samples?": [[169, "subset-the-samples"]], "Define a new variable based on others?": [[169, "define-a-new-variable-based-on-others"]], "Get summary stats?": [[169, "get-summary-stats"]], "Filter variants?": [[169, "filter-variants"]], "Find which new variables were added by a method?": [[169, "find-which-new-variables-were-added-by-a-method"]], "Save results to a Zarr file?": [[169, "save-results-to-a-zarr-file"]], "Load a dataset from Zarr?": [[169, "load-a-dataset-from-zarr"]], "sgkit: Statistical genetics toolkit in Python": [[170, "sgkit-statistical-genetics-toolkit-in-python"]], "Contents": [[170, null]], "Indices and tables": [[170, "indices-and-tables"]], "News": [[171, "news"]], "Introducing sgkit": [[172, "introducing-sgkit"]], "User Guide": [[173, "user-guide"]], "Reading and writing genetic data": [[173, "reading-and-writing-genetic-data"]], "Converting genetic data to Zarr": [[173, "converting-genetic-data-to-zarr"]], "VCF": [[173, "vcf"]], "Working with cloud-native data": [[173, "working-with-cloud-native-data"]], "Datasets": [[173, "datasets"]], "Genetic variables": [[173, "genetic-variables"]], "Dataset merge behavior": [[173, "dataset-merge-behavior"]], "Interop with other Python libraries": [[173, "interop-with-other-python-libraries"]], "Custom naming conventions": [[173, "custom-naming-conventions"]], "Adding custom data to a Dataset": [[173, "adding-custom-data-to-a-dataset"]], "Custom Computations": [[173, "custom-computations"]], "PCA": [[173, "pca"]], "Deployment": [[173, "deployment"]], "Deploying sgkit on a cluster": [[173, "deploying-sgkit-on-a-cluster"]], "Using GPUs": [[173, "using-gpus"]], "Troubleshooting": [[173, "troubleshooting"]], "Monitoring operations": [[173, "monitoring-operations"]], "Visualizing computations": [[173, "visualizing-computations"]], "Disabling the Numba cache": [[173, "disabling-the-numba-cache"]], "Reading VCF": [[174, "reading-vcf"]], "Highlights": [[174, "highlights"]], "Usage": [[174, "usage"]], "Multiple files": [[174, "multiple-files"]], "Partitioning": [[174, "partitioning"]], "Chunk sizes": [[174, "chunk-sizes"]], "Cloud storage": [[174, "cloud-storage"]], "Compression": [[174, "compression"]], "Low-level operation": [[174, "low-level-operation"]], "Polyploid and mixed-ploidy VCF": [[174, "polyploid-and-mixed-ploidy-vcf"]], "Example: converting 1000 genomes VCF to Zarr": [[174, "example-converting-1000-genomes-vcf-to-zarr"]], "Install sgkit": [[174, "install-sgkit"]], "Download the data": [[174, "download-the-data"]], "Run the conversion": [[174, "run-the-conversion"]], "Inspect the dataset": [[174, "inspect-the-dataset"]]}, "indexentries": {"fst() (in module sgkit)": [[7, "sgkit.Fst"]], "garud_h() (in module sgkit)": [[8, "sgkit.Garud_H"]], "tajimas_d() (in module sgkit)": [[9, "sgkit.Tajimas_D"]], "weir_goudet_beta() (in module sgkit)": [[10, "sgkit.Weir_Goudet_beta"]], "call_allele_frequencies() (in module sgkit)": [[11, "sgkit.call_allele_frequencies"]], "cohort_allele_frequencies() (in module sgkit)": [[12, "sgkit.cohort_allele_frequencies"]], "convert_call_to_index() (in module sgkit)": [[13, "sgkit.convert_call_to_index"]], "convert_probability_to_call() (in module sgkit)": [[14, "sgkit.convert_probability_to_call"]], "count_call_alleles() (in module sgkit)": [[15, "sgkit.count_call_alleles"]], "count_cohort_alleles() (in module sgkit)": [[16, "sgkit.count_cohort_alleles"]], "count_variant_alleles() (in module sgkit)": [[17, "sgkit.count_variant_alleles"]], "count_variant_genotypes() (in module sgkit)": [[18, "sgkit.count_variant_genotypes"]], "display_genotypes() (in module sgkit)": [[19, "sgkit.display_genotypes"]], "display_pedigree() (in module sgkit)": [[20, "sgkit.display_pedigree"]], "divergence() (in module sgkit)": [[21, "sgkit.divergence"]], "diversity() (in module sgkit)": [[22, "sgkit.diversity"]], "filter_partial_calls() (in module sgkit)": [[23, "sgkit.filter_partial_calls"]], "genee() (in module sgkit)": [[24, "sgkit.genee"]], "genomic_relationship() (in module sgkit)": [[25, "sgkit.genomic_relationship"]], "gwas_linear_regression() (in module sgkit)": [[26, "sgkit.gwas_linear_regression"]], "hardy_weinberg_test() (in module sgkit)": [[27, "sgkit.hardy_weinberg_test"]], "hybrid_inverse_relationship() (in module sgkit)": [[28, "sgkit.hybrid_inverse_relationship"]], "hybrid_relationship() (in module sgkit)": [[29, "sgkit.hybrid_relationship"]], "identity_by_state() (in module sgkit)": [[30, "sgkit.identity_by_state"]], "individual_heterozygosity() (in module sgkit)": [[31, "sgkit.individual_heterozygosity"]], "infer_call_ploidy() (in module sgkit)": [[32, "sgkit.infer_call_ploidy"]], "infer_sample_ploidy() (in module sgkit)": [[33, "sgkit.infer_sample_ploidy"]], "infer_variant_ploidy() (in module sgkit)": [[34, "sgkit.infer_variant_ploidy"]], "invert_relationship_matrix() (in module sgkit)": [[35, "sgkit.invert_relationship_matrix"]], "bgen_to_zarr() (in module sgkit.io.bgen)": [[36, "sgkit.io.bgen.bgen_to_zarr"]], "read_bgen() (in module sgkit.io.bgen)": [[37, "sgkit.io.bgen.read_bgen"]], "rechunk_bgen() (in module sgkit.io.bgen)": [[38, "sgkit.io.bgen.rechunk_bgen"]], "plink_to_zarr() (in module sgkit.io.plink)": [[39, "sgkit.io.plink.plink_to_zarr"]], "read_plink() (in module sgkit.io.plink)": [[40, "sgkit.io.plink.read_plink"]], "write_plink() (in module sgkit.io.plink)": [[41, "sgkit.io.plink.write_plink"]], "zarr_to_plink() (in module sgkit.io.plink)": [[42, "sgkit.io.plink.zarr_to_plink"]], "concat_zarrs() (in module sgkit.io.vcf)": [[43, "sgkit.io.vcf.concat_zarrs"]], "partition_into_regions() (in module sgkit.io.vcf)": [[44, "sgkit.io.vcf.partition_into_regions"]], "read_vcf() (in module sgkit.io.vcf)": [[45, "sgkit.io.vcf.read_vcf"]], "vcf_to_zarr() (in module sgkit.io.vcf)": [[46, "sgkit.io.vcf.vcf_to_zarr"]], "vcf_to_zarrs() (in module sgkit.io.vcf)": [[47, "sgkit.io.vcf.vcf_to_zarrs"]], "write_vcf() (in module sgkit.io.vcf)": [[48, "sgkit.io.vcf.write_vcf"]], "zarr_array_sizes() (in module sgkit.io.vcf)": [[49, "sgkit.io.vcf.zarr_array_sizes"]], "zarr_to_vcf() (in module sgkit.io.vcf)": [[50, "sgkit.io.vcf.zarr_to_vcf"]], "ld_matrix() (in module sgkit)": [[51, "sgkit.ld_matrix"]], "ld_prune() (in module sgkit)": [[52, "sgkit.ld_prune"]], "load_dataset() (in module sgkit)": [[53, "sgkit.load_dataset"]], "maximal_independent_set() (in module sgkit)": [[54, "sgkit.maximal_independent_set"]], "observed_heterozygosity() (in module sgkit)": [[55, "sgkit.observed_heterozygosity"]], "pairwise_distance() (in module sgkit)": [[56, "sgkit.pairwise_distance"]], "parent_indices() (in module sgkit)": [[57, "sgkit.parent_indices"]], "pbs() (in module sgkit)": [[58, "sgkit.pbs"]], "pc_relate() (in module sgkit)": [[59, "sgkit.pc_relate"]], "pedigree_contribution() (in module sgkit)": [[60, "sgkit.pedigree_contribution"]], "pedigree_inbreeding() (in module sgkit)": [[61, "sgkit.pedigree_inbreeding"]], "pedigree_inverse_kinship() (in module sgkit)": [[62, "sgkit.pedigree_inverse_kinship"]], "pedigree_kinship() (in module sgkit)": [[63, "sgkit.pedigree_kinship"]], "pedigree_sel() (in module sgkit)": [[64, "sgkit.pedigree_sel"]], "read_scikit_allel_vcfzarr() (in module sgkit)": [[65, "sgkit.read_scikit_allel_vcfzarr"]], "regenie() (in module sgkit)": [[66, "sgkit.regenie"]], "sample_stats() (in module sgkit)": [[67, "sgkit.sample_stats"]], "save_dataset() (in module sgkit)": [[68, "sgkit.save_dataset"]], "simulate_genedrop() (in module sgkit)": [[69, "sgkit.simulate_genedrop"]], "simulate_genotype_call_dataset() (in module sgkit)": [[70, "sgkit.simulate_genotype_call_dataset"]], "call_allele_count_spec (in module sgkit.variables)": [[71, "sgkit.variables.call_allele_count_spec"]], "call_allele_frequency_spec (in module sgkit.variables)": [[72, "sgkit.variables.call_allele_frequency_spec"]], "call_dosage_mask_spec (in module sgkit.variables)": [[73, "sgkit.variables.call_dosage_mask_spec"]], "call_dosage_spec (in module sgkit.variables)": [[74, "sgkit.variables.call_dosage_spec"]], "call_genotype_complete_mask_spec (in module sgkit.variables)": [[75, "sgkit.variables.call_genotype_complete_mask_spec"]], "call_genotype_complete_spec (in module sgkit.variables)": [[76, "sgkit.variables.call_genotype_complete_spec"]], "call_genotype_fill_spec (in module sgkit.variables)": [[77, "sgkit.variables.call_genotype_fill_spec"]], "call_genotype_index_mask_spec (in module sgkit.variables)": [[78, "sgkit.variables.call_genotype_index_mask_spec"]], "call_genotype_index_spec (in module sgkit.variables)": [[79, "sgkit.variables.call_genotype_index_spec"]], "call_genotype_mask_spec (in module sgkit.variables)": [[80, "sgkit.variables.call_genotype_mask_spec"]], "call_genotype_phased_spec (in module sgkit.variables)": [[81, "sgkit.variables.call_genotype_phased_spec"]], "call_genotype_probability_mask_spec (in module sgkit.variables)": [[82, "sgkit.variables.call_genotype_probability_mask_spec"]], "call_genotype_probability_spec (in module sgkit.variables)": [[83, "sgkit.variables.call_genotype_probability_spec"]], "call_genotype_spec (in module sgkit.variables)": [[84, "sgkit.variables.call_genotype_spec"]], "call_heterozygosity_spec (in module sgkit.variables)": [[85, "sgkit.variables.call_heterozygosity_spec"]], "call_ploidy_spec (in module sgkit.variables)": [[86, "sgkit.variables.call_ploidy_spec"]], "cohort_allele_count_spec (in module sgkit.variables)": [[87, "sgkit.variables.cohort_allele_count_spec"]], "cohort_allele_frequency_spec (in module sgkit.variables)": [[88, "sgkit.variables.cohort_allele_frequency_spec"]], "covariates_spec (in module sgkit.variables)": [[89, "sgkit.variables.covariates_spec"]], "interval_contig_name_spec (in module sgkit.variables)": [[90, "sgkit.variables.interval_contig_name_spec"]], "interval_start_spec (in module sgkit.variables)": [[91, "sgkit.variables.interval_start_spec"]], "interval_stop_spec (in module sgkit.variables)": [[92, "sgkit.variables.interval_stop_spec"]], "ld_prune_index_to_drop_spec (in module sgkit.variables)": [[93, "sgkit.variables.ld_prune_index_to_drop_spec"]], "parent_id_spec (in module sgkit.variables)": [[94, "sgkit.variables.parent_id_spec"]], "parent_spec (in module sgkit.variables)": [[95, "sgkit.variables.parent_spec"]], "pc_relate_phi_spec (in module sgkit.variables)": [[96, "sgkit.variables.pc_relate_phi_spec"]], "regenie_base_prediction_spec (in module sgkit.variables)": [[97, "sgkit.variables.regenie_base_prediction_spec"]], "regenie_loco_prediction_spec (in module sgkit.variables)": [[98, "sgkit.variables.regenie_loco_prediction_spec"]], "regenie_meta_prediction_spec (in module sgkit.variables)": [[99, "sgkit.variables.regenie_meta_prediction_spec"]], "sample_call_rate_spec (in module sgkit.variables)": [[100, "sgkit.variables.sample_call_rate_spec"]], "sample_cohort_spec (in module sgkit.variables)": [[101, "sgkit.variables.sample_cohort_spec"]], "sample_id_spec (in module sgkit.variables)": [[102, "sgkit.variables.sample_id_spec"]], "sample_n_called_spec (in module sgkit.variables)": [[103, "sgkit.variables.sample_n_called_spec"]], "sample_n_het_spec (in module sgkit.variables)": [[104, "sgkit.variables.sample_n_het_spec"]], "sample_n_hom_alt_spec (in module sgkit.variables)": [[105, "sgkit.variables.sample_n_hom_alt_spec"]], "sample_n_hom_ref_spec (in module sgkit.variables)": [[106, "sgkit.variables.sample_n_hom_ref_spec"]], "sample_n_non_ref_spec (in module sgkit.variables)": [[107, "sgkit.variables.sample_n_non_ref_spec"]], "sample_pca_component_spec (in module sgkit.variables)": [[108, "sgkit.variables.sample_pca_component_spec"]], "sample_pca_explained_variance_ratio_spec (in module sgkit.variables)": [[109, "sgkit.variables.sample_pca_explained_variance_ratio_spec"]], "sample_pca_explained_variance_spec (in module sgkit.variables)": [[110, "sgkit.variables.sample_pca_explained_variance_spec"]], "sample_pca_loading_spec (in module sgkit.variables)": [[111, "sgkit.variables.sample_pca_loading_spec"]], "sample_pca_projection_spec (in module sgkit.variables)": [[112, "sgkit.variables.sample_pca_projection_spec"]], "sample_ploidy_spec (in module sgkit.variables)": [[113, "sgkit.variables.sample_ploidy_spec"]], "stat_fst_spec (in module sgkit.variables)": [[114, "sgkit.variables.stat_Fst_spec"]], "stat_garud_h123_spec (in module sgkit.variables)": [[115, "sgkit.variables.stat_Garud_h123_spec"]], "stat_garud_h12_spec (in module sgkit.variables)": [[116, "sgkit.variables.stat_Garud_h12_spec"]], "stat_garud_h1_spec (in module sgkit.variables)": [[117, "sgkit.variables.stat_Garud_h1_spec"]], "stat_garud_h2_h1_spec (in module sgkit.variables)": [[118, "sgkit.variables.stat_Garud_h2_h1_spec"]], "stat_hamilton_kerr_lambda_spec (in module sgkit.variables)": [[119, "sgkit.variables.stat_Hamilton_Kerr_lambda_spec"]], "stat_hamilton_kerr_tau_spec (in module sgkit.variables)": [[120, "sgkit.variables.stat_Hamilton_Kerr_tau_spec"]], "stat_tajimas_d_spec (in module sgkit.variables)": [[121, "sgkit.variables.stat_Tajimas_D_spec"]], "stat_weir_goudet_beta_spec (in module sgkit.variables)": [[122, "sgkit.variables.stat_Weir_Goudet_beta_spec"]], "stat_divergence_spec (in module sgkit.variables)": [[123, "sgkit.variables.stat_divergence_spec"]], "stat_diversity_spec (in module sgkit.variables)": [[124, "sgkit.variables.stat_diversity_spec"]], "stat_genomic_kinship_spec (in module sgkit.variables)": [[125, "sgkit.variables.stat_genomic_kinship_spec"]], "stat_genomic_relationship_spec (in module sgkit.variables)": [[126, "sgkit.variables.stat_genomic_relationship_spec"]], "stat_hybrid_inverse_relationship_spec (in module sgkit.variables)": [[127, "sgkit.variables.stat_hybrid_inverse_relationship_spec"]], "stat_hybrid_relationship_spec (in module sgkit.variables)": [[128, "sgkit.variables.stat_hybrid_relationship_spec"]], "stat_identity_by_state_spec (in module sgkit.variables)": [[129, "sgkit.variables.stat_identity_by_state_spec"]], "stat_inverse_relationship_spec (in module sgkit.variables)": [[130, "sgkit.variables.stat_inverse_relationship_spec"]], "stat_observed_heterozygosity_spec (in module sgkit.variables)": [[131, "sgkit.variables.stat_observed_heterozygosity_spec"]], "stat_pbs_spec (in module sgkit.variables)": [[132, "sgkit.variables.stat_pbs_spec"]], "stat_pedigree_contribution_spec (in module sgkit.variables)": [[133, "sgkit.variables.stat_pedigree_contribution_spec"]], "stat_pedigree_inbreeding_spec (in module sgkit.variables)": [[134, "sgkit.variables.stat_pedigree_inbreeding_spec"]], "stat_pedigree_inverse_kinship_spec (in module sgkit.variables)": [[135, "sgkit.variables.stat_pedigree_inverse_kinship_spec"]], "stat_pedigree_inverse_relationship_spec (in module sgkit.variables)": [[136, "sgkit.variables.stat_pedigree_inverse_relationship_spec"]], "stat_pedigree_kinship_spec (in module sgkit.variables)": [[137, "sgkit.variables.stat_pedigree_kinship_spec"]], "stat_pedigree_relationship_spec (in module sgkit.variables)": [[138, "sgkit.variables.stat_pedigree_relationship_spec"]], "traits_spec (in module sgkit.variables)": [[139, "sgkit.variables.traits_spec"]], "variant_allele_count_spec (in module sgkit.variables)": [[140, "sgkit.variables.variant_allele_count_spec"]], "variant_allele_frequency_spec (in module sgkit.variables)": [[141, "sgkit.variables.variant_allele_frequency_spec"]], "variant_allele_spec (in module sgkit.variables)": [[142, "sgkit.variables.variant_allele_spec"]], "variant_allele_total_spec (in module sgkit.variables)": [[143, "sgkit.variables.variant_allele_total_spec"]], "variant_call_rate_spec (in module sgkit.variables)": [[144, "sgkit.variables.variant_call_rate_spec"]], "variant_contig_spec (in module sgkit.variables)": [[145, "sgkit.variables.variant_contig_spec"]], "variant_genotype_count_spec (in module sgkit.variables)": [[146, "sgkit.variables.variant_genotype_count_spec"]], "variant_hwe_p_value_spec (in module sgkit.variables)": [[147, "sgkit.variables.variant_hwe_p_value_spec"]], "variant_id_spec (in module sgkit.variables)": [[148, "sgkit.variables.variant_id_spec"]], "variant_linreg_beta_spec (in module sgkit.variables)": [[149, "sgkit.variables.variant_linreg_beta_spec"]], "variant_linreg_p_value_spec (in module sgkit.variables)": [[150, "sgkit.variables.variant_linreg_p_value_spec"]], "variant_linreg_t_value_spec (in module sgkit.variables)": [[151, "sgkit.variables.variant_linreg_t_value_spec"]], "variant_n_called_spec (in module sgkit.variables)": [[152, "sgkit.variables.variant_n_called_spec"]], "variant_n_het_spec (in module sgkit.variables)": [[153, "sgkit.variables.variant_n_het_spec"]], "variant_n_hom_alt_spec (in module sgkit.variables)": [[154, "sgkit.variables.variant_n_hom_alt_spec"]], "variant_n_hom_ref_spec (in module sgkit.variables)": [[155, "sgkit.variables.variant_n_hom_ref_spec"]], "variant_n_non_ref_spec (in module sgkit.variables)": [[156, "sgkit.variables.variant_n_non_ref_spec"]], "variant_ploidy_spec (in module sgkit.variables)": [[157, "sgkit.variables.variant_ploidy_spec"]], "variant_position_spec (in module sgkit.variables)": [[158, "sgkit.variables.variant_position_spec"]], "variant_score_spec (in module sgkit.variables)": [[159, "sgkit.variables.variant_score_spec"]], "window_contig_spec (in module sgkit.variables)": [[160, "sgkit.variables.window_contig_spec"]], "window_start_spec (in module sgkit.variables)": [[161, "sgkit.variables.window_start_spec"]], "window_stop_spec (in module sgkit.variables)": [[162, "sgkit.variables.window_stop_spec"]], "variant_stats() (in module sgkit)": [[163, "sgkit.variant_stats"]], "window_by_genome() (in module sgkit)": [[164, "sgkit.window_by_genome"]], "window_by_interval() (in module sgkit)": [[165, "sgkit.window_by_interval"]], "window_by_position() (in module sgkit)": [[166, "sgkit.window_by_position"]], "window_by_variant() (in module sgkit)": [[167, "sgkit.window_by_variant"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["about", "api", "changelog", "contributing", "examples/gwas_tutorial", "examples/index", "examples/relatedness_tutorial", "generated/sgkit.Fst", "generated/sgkit.Garud_H", "generated/sgkit.Tajimas_D", "generated/sgkit.Weir_Goudet_beta", "generated/sgkit.call_allele_frequencies", "generated/sgkit.cohort_allele_frequencies", "generated/sgkit.convert_call_to_index", "generated/sgkit.convert_probability_to_call", "generated/sgkit.count_call_alleles", "generated/sgkit.count_cohort_alleles", "generated/sgkit.count_variant_alleles", "generated/sgkit.count_variant_genotypes", "generated/sgkit.display_genotypes", "generated/sgkit.display_pedigree", "generated/sgkit.divergence", "generated/sgkit.diversity", "generated/sgkit.filter_partial_calls", "generated/sgkit.genee", "generated/sgkit.genomic_relationship", "generated/sgkit.gwas_linear_regression", "generated/sgkit.hardy_weinberg_test", "generated/sgkit.hybrid_inverse_relationship", "generated/sgkit.hybrid_relationship", "generated/sgkit.identity_by_state", "generated/sgkit.individual_heterozygosity", "generated/sgkit.infer_call_ploidy", "generated/sgkit.infer_sample_ploidy", "generated/sgkit.infer_variant_ploidy", "generated/sgkit.invert_relationship_matrix", "generated/sgkit.io.bgen.bgen_to_zarr", "generated/sgkit.io.bgen.read_bgen", "generated/sgkit.io.bgen.rechunk_bgen", "generated/sgkit.io.plink.plink_to_zarr", "generated/sgkit.io.plink.read_plink", "generated/sgkit.io.plink.write_plink", "generated/sgkit.io.plink.zarr_to_plink", "generated/sgkit.io.vcf.concat_zarrs", "generated/sgkit.io.vcf.partition_into_regions", "generated/sgkit.io.vcf.read_vcf", "generated/sgkit.io.vcf.vcf_to_zarr", "generated/sgkit.io.vcf.vcf_to_zarrs", "generated/sgkit.io.vcf.write_vcf", "generated/sgkit.io.vcf.zarr_array_sizes", "generated/sgkit.io.vcf.zarr_to_vcf", "generated/sgkit.ld_matrix", "generated/sgkit.ld_prune", "generated/sgkit.load_dataset", 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dependencies": [[3, "python-dependencies"]], "Contributing to documentation": [[3, "contributing-to-documentation"]], "Benchmarks": [[3, "benchmarks"]], "Review process": [[3, "review-process"]], "Design discussions": [[3, "design-discussions"]], "Dataset subclassing": [[3, "dataset-subclassing"]], "Dataset API typing": [[3, "dataset-api-typing"]], "Dataset variables": [[3, "dataset-variables"]], "Delayed invariant checks": [[3, "delayed-invariant-checks"]], "Mixed ploidy": [[3, "mixed-ploidy"]], "Numba guvectorize usage": [[3, "numba-guvectorize-usage"]], "API namespace": [[3, "api-namespace"]], "GWAS Tutorial": [[4, "gwas-tutorial"]], "Download public 1000 Genomes data": [[4, "download-public-1000-genomes-data"]], "Importing data from VCF": [[4, "importing-data-from-vcf"]], "Getting to know our data": [[4, "getting-to-know-our-data"]], "Adding column fields": [[4, "adding-column-fields"]], "Query functions": [[4, "query-functions"]], "Quality control": [[4, "quality-control"]], "Let\u2019s do a GWAS!": [[4, "let-s-do-a-gwas"]], "Confounded!": [[4, "confounded"]], "Examples": [[5, "examples"]], "Relatedness Tutorial": [[6, "relatedness-tutorial"]], "Download the pig dataset": [[6, "download-the-pig-dataset"]], "Reading pedigree data": [[6, "reading-pedigree-data"]], "Working with pedigree data": [[6, "working-with-pedigree-data"]], "Pedigree relationships": [[6, "pedigree-relationships"]], "Genomic relationships": [[6, "genomic-relationships"]], "The VanRaden GRM": [[6, "the-vanraden-grm"]], "A better estimate of ancestral allele frequencies": [[6, "a-better-estimate-of-ancestral-allele-frequencies"]], "Weir-Goudet GRM": [[6, "weir-goudet-grm"]], "Hybrid relationship matrices": [[6, "hybrid-relationship-matrices"]], "References": [[6, "references"]], "sgkit.Fst": [[7, "sgkit-fst"]], "sgkit.Garud_H": [[8, "sgkit-garud-h"]], "sgkit.Tajimas_D": [[9, "sgkit-tajimas-d"]], "sgkit.Weir_Goudet_beta": [[10, "sgkit-weir-goudet-beta"]], "sgkit.call_allele_frequencies": [[11, "sgkit-call-allele-frequencies"]], "sgkit.cohort_allele_frequencies": [[12, "sgkit-cohort-allele-frequencies"]], "sgkit.convert_call_to_index": [[13, "sgkit-convert-call-to-index"]], "sgkit.convert_probability_to_call": [[14, "sgkit-convert-probability-to-call"]], "sgkit.count_call_alleles": [[15, "sgkit-count-call-alleles"]], "sgkit.count_cohort_alleles": [[16, "sgkit-count-cohort-alleles"]], "sgkit.count_variant_alleles": [[17, "sgkit-count-variant-alleles"]], "sgkit.count_variant_genotypes": [[18, "sgkit-count-variant-genotypes"]], "sgkit.display_genotypes": [[19, "sgkit-display-genotypes"]], "sgkit.display_pedigree": [[20, "sgkit-display-pedigree"]], "sgkit.divergence": [[21, "sgkit-divergence"]], "sgkit.diversity": [[22, "sgkit-diversity"]], "sgkit.filter_partial_calls": [[23, "sgkit-filter-partial-calls"]], "sgkit.genee": [[24, "sgkit-genee"]], "sgkit.genomic_relationship": [[25, "sgkit-genomic-relationship"]], "sgkit.gwas_linear_regression": [[26, "sgkit-gwas-linear-regression"]], "sgkit.hardy_weinberg_test": [[27, "sgkit-hardy-weinberg-test"]], "sgkit.hybrid_inverse_relationship": [[28, "sgkit-hybrid-inverse-relationship"]], "sgkit.hybrid_relationship": [[29, "sgkit-hybrid-relationship"]], "sgkit.identity_by_state": [[30, "sgkit-identity-by-state"]], "sgkit.individual_heterozygosity": [[31, "sgkit-individual-heterozygosity"]], "sgkit.infer_call_ploidy": [[32, "sgkit-infer-call-ploidy"]], "sgkit.infer_sample_ploidy": [[33, "sgkit-infer-sample-ploidy"]], "sgkit.infer_variant_ploidy": [[34, "sgkit-infer-variant-ploidy"]], "sgkit.invert_relationship_matrix": [[35, "sgkit-invert-relationship-matrix"]], "sgkit.io.bgen.bgen_to_zarr": [[36, "sgkit-io-bgen-bgen-to-zarr"]], "sgkit.io.bgen.read_bgen": [[37, "sgkit-io-bgen-read-bgen"]], "sgkit.io.bgen.rechunk_bgen": [[38, "sgkit-io-bgen-rechunk-bgen"]], "sgkit.io.plink.plink_to_zarr": [[39, "sgkit-io-plink-plink-to-zarr"]], "sgkit.io.plink.read_plink": [[40, "sgkit-io-plink-read-plink"]], "sgkit.io.plink.write_plink": [[41, "sgkit-io-plink-write-plink"]], "sgkit.io.plink.zarr_to_plink": [[42, "sgkit-io-plink-zarr-to-plink"]], "sgkit.io.vcf.concat_zarrs": [[43, "sgkit-io-vcf-concat-zarrs"]], "sgkit.io.vcf.partition_into_regions": [[44, "sgkit-io-vcf-partition-into-regions"]], "sgkit.io.vcf.read_vcf": [[45, "sgkit-io-vcf-read-vcf"]], "sgkit.io.vcf.vcf_to_zarr": [[46, "sgkit-io-vcf-vcf-to-zarr"]], "sgkit.io.vcf.vcf_to_zarrs": [[47, "sgkit-io-vcf-vcf-to-zarrs"]], "sgkit.io.vcf.write_vcf": [[48, "sgkit-io-vcf-write-vcf"]], "sgkit.io.vcf.zarr_array_sizes": [[49, "sgkit-io-vcf-zarr-array-sizes"]], "sgkit.io.vcf.zarr_to_vcf": [[50, "sgkit-io-vcf-zarr-to-vcf"]], "sgkit.ld_matrix": [[51, "sgkit-ld-matrix"]], "sgkit.ld_prune": [[52, "sgkit-ld-prune"]], "sgkit.load_dataset": [[53, "sgkit-load-dataset"]], "sgkit.maximal_independent_set": [[54, "sgkit-maximal-independent-set"]], "sgkit.observed_heterozygosity": [[55, "sgkit-observed-heterozygosity"]], "sgkit.pairwise_distance": [[56, "sgkit-pairwise-distance"]], "sgkit.parent_indices": [[57, "sgkit-parent-indices"]], "sgkit.pbs": [[58, "sgkit-pbs"]], "sgkit.pc_relate": [[59, "sgkit-pc-relate"]], "sgkit.pedigree_contribution": [[60, "sgkit-pedigree-contribution"]], "sgkit.pedigree_inbreeding": [[61, "sgkit-pedigree-inbreeding"]], "sgkit.pedigree_inverse_kinship": [[62, "sgkit-pedigree-inverse-kinship"]], "sgkit.pedigree_kinship": [[63, "sgkit-pedigree-kinship"]], "sgkit.pedigree_sel": [[64, "sgkit-pedigree-sel"]], "sgkit.read_scikit_allel_vcfzarr": [[65, "sgkit-read-scikit-allel-vcfzarr"]], "sgkit.regenie": [[66, "sgkit-regenie"]], "sgkit.sample_stats": [[67, "sgkit-sample-stats"]], "sgkit.save_dataset": [[68, "sgkit-save-dataset"]], "sgkit.simulate_genedrop": [[69, "sgkit-simulate-genedrop"]], "sgkit.simulate_genotype_call_dataset": [[70, "sgkit-simulate-genotype-call-dataset"]], "sgkit.variables.call_allele_count_spec": [[71, "sgkit-variables-call-allele-count-spec"]], "sgkit.variables.call_allele_frequency_spec": [[72, "sgkit-variables-call-allele-frequency-spec"]], "sgkit.variables.call_dosage_mask_spec": [[73, "sgkit-variables-call-dosage-mask-spec"]], "sgkit.variables.call_dosage_spec": [[74, "sgkit-variables-call-dosage-spec"]], "sgkit.variables.call_genotype_complete_mask_spec": [[75, "sgkit-variables-call-genotype-complete-mask-spec"]], "sgkit.variables.call_genotype_complete_spec": [[76, "sgkit-variables-call-genotype-complete-spec"]], "sgkit.variables.call_genotype_fill_spec": [[77, "sgkit-variables-call-genotype-fill-spec"]], "sgkit.variables.call_genotype_index_mask_spec": [[78, "sgkit-variables-call-genotype-index-mask-spec"]], "sgkit.variables.call_genotype_index_spec": [[79, "sgkit-variables-call-genotype-index-spec"]], "sgkit.variables.call_genotype_mask_spec": [[80, "sgkit-variables-call-genotype-mask-spec"]], "sgkit.variables.call_genotype_phased_spec": [[81, "sgkit-variables-call-genotype-phased-spec"]], "sgkit.variables.call_genotype_probability_mask_spec": [[82, "sgkit-variables-call-genotype-probability-mask-spec"]], "sgkit.variables.call_genotype_probability_spec": [[83, "sgkit-variables-call-genotype-probability-spec"]], "sgkit.variables.call_genotype_spec": [[84, "sgkit-variables-call-genotype-spec"]], "sgkit.variables.call_heterozygosity_spec": [[85, "sgkit-variables-call-heterozygosity-spec"]], "sgkit.variables.call_ploidy_spec": [[86, "sgkit-variables-call-ploidy-spec"]], "sgkit.variables.cohort_allele_count_spec": [[87, "sgkit-variables-cohort-allele-count-spec"]], "sgkit.variables.cohort_allele_frequency_spec": [[88, "sgkit-variables-cohort-allele-frequency-spec"]], "sgkit.variables.covariates_spec": [[89, "sgkit-variables-covariates-spec"]], "sgkit.variables.interval_contig_name_spec": [[90, "sgkit-variables-interval-contig-name-spec"]], "sgkit.variables.interval_start_spec": [[91, "sgkit-variables-interval-start-spec"]], "sgkit.variables.interval_stop_spec": [[92, "sgkit-variables-interval-stop-spec"]], "sgkit.variables.ld_prune_index_to_drop_spec": [[93, "sgkit-variables-ld-prune-index-to-drop-spec"]], "sgkit.variables.parent_id_spec": [[94, "sgkit-variables-parent-id-spec"]], "sgkit.variables.parent_spec": [[95, "sgkit-variables-parent-spec"]], "sgkit.variables.pc_relate_phi_spec": [[96, "sgkit-variables-pc-relate-phi-spec"]], "sgkit.variables.regenie_base_prediction_spec": [[97, "sgkit-variables-regenie-base-prediction-spec"]], "sgkit.variables.regenie_loco_prediction_spec": [[98, "sgkit-variables-regenie-loco-prediction-spec"]], "sgkit.variables.regenie_meta_prediction_spec": [[99, "sgkit-variables-regenie-meta-prediction-spec"]], "sgkit.variables.sample_call_rate_spec": [[100, "sgkit-variables-sample-call-rate-spec"]], "sgkit.variables.sample_cohort_spec": [[101, "sgkit-variables-sample-cohort-spec"]], "sgkit.variables.sample_id_spec": [[102, "sgkit-variables-sample-id-spec"]], "sgkit.variables.sample_n_called_spec": [[103, "sgkit-variables-sample-n-called-spec"]], "sgkit.variables.sample_n_het_spec": [[104, "sgkit-variables-sample-n-het-spec"]], "sgkit.variables.sample_n_hom_alt_spec": [[105, "sgkit-variables-sample-n-hom-alt-spec"]], "sgkit.variables.sample_n_hom_ref_spec": [[106, "sgkit-variables-sample-n-hom-ref-spec"]], "sgkit.variables.sample_n_non_ref_spec": [[107, "sgkit-variables-sample-n-non-ref-spec"]], "sgkit.variables.sample_pca_component_spec": [[108, "sgkit-variables-sample-pca-component-spec"]], "sgkit.variables.sample_pca_explained_variance_ratio_spec": [[109, "sgkit-variables-sample-pca-explained-variance-ratio-spec"]], "sgkit.variables.sample_pca_explained_variance_spec": [[110, "sgkit-variables-sample-pca-explained-variance-spec"]], "sgkit.variables.sample_pca_loading_spec": [[111, "sgkit-variables-sample-pca-loading-spec"]], "sgkit.variables.sample_pca_projection_spec": [[112, "sgkit-variables-sample-pca-projection-spec"]], "sgkit.variables.sample_ploidy_spec": [[113, "sgkit-variables-sample-ploidy-spec"]], "sgkit.variables.stat_Fst_spec": [[114, "sgkit-variables-stat-fst-spec"]], "sgkit.variables.stat_Garud_h123_spec": [[115, "sgkit-variables-stat-garud-h123-spec"]], "sgkit.variables.stat_Garud_h12_spec": [[116, "sgkit-variables-stat-garud-h12-spec"]], "sgkit.variables.stat_Garud_h1_spec": [[117, "sgkit-variables-stat-garud-h1-spec"]], "sgkit.variables.stat_Garud_h2_h1_spec": [[118, "sgkit-variables-stat-garud-h2-h1-spec"]], "sgkit.variables.stat_Hamilton_Kerr_lambda_spec": [[119, "sgkit-variables-stat-hamilton-kerr-lambda-spec"]], "sgkit.variables.stat_Hamilton_Kerr_tau_spec": [[120, "sgkit-variables-stat-hamilton-kerr-tau-spec"]], "sgkit.variables.stat_Tajimas_D_spec": [[121, "sgkit-variables-stat-tajimas-d-spec"]], "sgkit.variables.stat_Weir_Goudet_beta_spec": [[122, "sgkit-variables-stat-weir-goudet-beta-spec"]], "sgkit.variables.stat_divergence_spec": [[123, "sgkit-variables-stat-divergence-spec"]], "sgkit.variables.stat_diversity_spec": [[124, "sgkit-variables-stat-diversity-spec"]], "sgkit.variables.stat_genomic_kinship_spec": [[125, "sgkit-variables-stat-genomic-kinship-spec"]], "sgkit.variables.stat_genomic_relationship_spec": [[126, "sgkit-variables-stat-genomic-relationship-spec"]], "sgkit.variables.stat_hybrid_inverse_relationship_spec": [[127, "sgkit-variables-stat-hybrid-inverse-relationship-spec"]], "sgkit.variables.stat_hybrid_relationship_spec": [[128, "sgkit-variables-stat-hybrid-relationship-spec"]], "sgkit.variables.stat_identity_by_state_spec": [[129, "sgkit-variables-stat-identity-by-state-spec"]], "sgkit.variables.stat_inverse_relationship_spec": [[130, "sgkit-variables-stat-inverse-relationship-spec"]], "sgkit.variables.stat_observed_heterozygosity_spec": [[131, "sgkit-variables-stat-observed-heterozygosity-spec"]], "sgkit.variables.stat_pbs_spec": [[132, "sgkit-variables-stat-pbs-spec"]], "sgkit.variables.stat_pedigree_contribution_spec": [[133, "sgkit-variables-stat-pedigree-contribution-spec"]], "sgkit.variables.stat_pedigree_inbreeding_spec": [[134, "sgkit-variables-stat-pedigree-inbreeding-spec"]], "sgkit.variables.stat_pedigree_inverse_kinship_spec": [[135, "sgkit-variables-stat-pedigree-inverse-kinship-spec"]], "sgkit.variables.stat_pedigree_inverse_relationship_spec": [[136, "sgkit-variables-stat-pedigree-inverse-relationship-spec"]], "sgkit.variables.stat_pedigree_kinship_spec": [[137, "sgkit-variables-stat-pedigree-kinship-spec"]], "sgkit.variables.stat_pedigree_relationship_spec": [[138, "sgkit-variables-stat-pedigree-relationship-spec"]], "sgkit.variables.traits_spec": [[139, "sgkit-variables-traits-spec"]], "sgkit.variables.variant_allele_count_spec": [[140, "sgkit-variables-variant-allele-count-spec"]], "sgkit.variables.variant_allele_frequency_spec": [[141, "sgkit-variables-variant-allele-frequency-spec"]], "sgkit.variables.variant_allele_spec": [[142, "sgkit-variables-variant-allele-spec"]], "sgkit.variables.variant_allele_total_spec": [[143, "sgkit-variables-variant-allele-total-spec"]], "sgkit.variables.variant_call_rate_spec": [[144, "sgkit-variables-variant-call-rate-spec"]], "sgkit.variables.variant_contig_spec": [[145, "sgkit-variables-variant-contig-spec"]], "sgkit.variables.variant_genotype_count_spec": [[146, "sgkit-variables-variant-genotype-count-spec"]], "sgkit.variables.variant_hwe_p_value_spec": [[147, "sgkit-variables-variant-hwe-p-value-spec"]], "sgkit.variables.variant_id_spec": [[148, "sgkit-variables-variant-id-spec"]], "sgkit.variables.variant_linreg_beta_spec": [[149, "sgkit-variables-variant-linreg-beta-spec"]], "sgkit.variables.variant_linreg_p_value_spec": [[150, "sgkit-variables-variant-linreg-p-value-spec"]], "sgkit.variables.variant_linreg_t_value_spec": [[151, "sgkit-variables-variant-linreg-t-value-spec"]], "sgkit.variables.variant_n_called_spec": [[152, "sgkit-variables-variant-n-called-spec"]], "sgkit.variables.variant_n_het_spec": [[153, "sgkit-variables-variant-n-het-spec"]], "sgkit.variables.variant_n_hom_alt_spec": [[154, "sgkit-variables-variant-n-hom-alt-spec"]], "sgkit.variables.variant_n_hom_ref_spec": [[155, "sgkit-variables-variant-n-hom-ref-spec"]], "sgkit.variables.variant_n_non_ref_spec": [[156, "sgkit-variables-variant-n-non-ref-spec"]], "sgkit.variables.variant_ploidy_spec": [[157, "sgkit-variables-variant-ploidy-spec"]], "sgkit.variables.variant_position_spec": [[158, "sgkit-variables-variant-position-spec"]], "sgkit.variables.variant_score_spec": [[159, "sgkit-variables-variant-score-spec"]], "sgkit.variables.window_contig_spec": [[160, "sgkit-variables-window-contig-spec"]], "sgkit.variables.window_start_spec": [[161, "sgkit-variables-window-start-spec"]], "sgkit.variables.window_stop_spec": [[162, "sgkit-variables-window-stop-spec"]], "sgkit.variant_stats": [[163, "sgkit-variant-stats"]], "sgkit.window_by_genome": [[164, "sgkit-window-by-genome"]], "sgkit.window_by_interval": [[165, "sgkit-window-by-interval"]], "sgkit.window_by_position": [[166, "sgkit-window-by-position"]], "sgkit.window_by_variant": [[167, "sgkit-window-by-variant"]], "Getting Started": [[168, "getting-started"]], "Installation": [[168, "installation"], [173, "installation"], [174, "installation"]], "Overview": [[168, "overview"]], "Data structures": [[168, "data-structures"]], "Genetic methods": [[168, "genetic-methods"]], "Missing data": [[168, "missing-data"]], "Windowing": [[168, "windowing"]], "Cohorts": [[168, "cohorts"]], "Chaining operations": [[168, "chaining-operations"]], "Chunked arrays": [[168, "chunked-arrays"]], "How do I \u2026": [[169, "how-do-i"]], "Create a test dataset?": [[169, "create-a-test-dataset"]], "Look at the dataset summary?": [[169, "look-at-the-dataset-summary"]], "Get the values for a variable in a dataset?": [[169, "get-the-values-for-a-variable-in-a-dataset"]], "Find the definition for a variable in a dataset?": [[169, "find-the-definition-for-a-variable-in-a-dataset"]], "Look at the genotypes?": [[169, "look-at-the-genotypes"]], "Subset the variables?": [[169, "subset-the-variables"]], "Subset to a genomic range?": [[169, "subset-to-a-genomic-range"]], "Get the list of samples?": [[169, "get-the-list-of-samples"]], "Subset the samples?": [[169, "subset-the-samples"]], "Define a new variable based on others?": [[169, "define-a-new-variable-based-on-others"]], "Get summary stats?": [[169, "get-summary-stats"]], "Filter variants?": [[169, "filter-variants"]], "Find which new variables were added by a method?": [[169, "find-which-new-variables-were-added-by-a-method"]], "Save results to a Zarr file?": [[169, "save-results-to-a-zarr-file"]], "Load a dataset from Zarr?": [[169, "load-a-dataset-from-zarr"]], "sgkit: Statistical genetics toolkit in Python": [[170, "sgkit-statistical-genetics-toolkit-in-python"]], "Contents": [[170, null]], "Indices and tables": [[170, "indices-and-tables"]], "News": [[171, "news"]], "Introducing sgkit": [[172, "introducing-sgkit"]], "User Guide": [[173, "user-guide"]], "Reading and writing genetic data": [[173, "reading-and-writing-genetic-data"]], "Converting genetic data to Zarr": [[173, "converting-genetic-data-to-zarr"]], "VCF": [[173, "vcf"]], "Working with cloud-native data": [[173, "working-with-cloud-native-data"]], "Datasets": [[173, "datasets"]], "Genetic variables": [[173, "genetic-variables"]], "Dataset merge behavior": [[173, "dataset-merge-behavior"]], "Interop with other Python libraries": [[173, "interop-with-other-python-libraries"]], "Custom naming conventions": [[173, "custom-naming-conventions"]], "Adding custom data to a Dataset": [[173, "adding-custom-data-to-a-dataset"]], "Custom Computations": [[173, "custom-computations"]], "PCA": [[173, "pca"]], "Deployment": [[173, "deployment"]], "Deploying sgkit on a cluster": [[173, "deploying-sgkit-on-a-cluster"]], "Using GPUs": [[173, "using-gpus"]], "Troubleshooting": [[173, "troubleshooting"]], "Monitoring operations": [[173, "monitoring-operations"]], "Visualizing computations": [[173, "visualizing-computations"]], "Disabling the Numba cache": [[173, "disabling-the-numba-cache"]], "Reading VCF": [[174, "reading-vcf"]], "Highlights": [[174, "highlights"]], "Usage": [[174, "usage"]], "Multiple files": [[174, "multiple-files"]], "Partitioning": [[174, "partitioning"]], "Chunk sizes": [[174, "chunk-sizes"]], "Cloud storage": [[174, "cloud-storage"]], "Compression": [[174, "compression"]], "Low-level operation": [[174, "low-level-operation"]], "Polyploid and mixed-ploidy VCF": [[174, "polyploid-and-mixed-ploidy-vcf"]], "Example: converting 1000 genomes VCF to Zarr": [[174, "example-converting-1000-genomes-vcf-to-zarr"]], "Install sgkit": [[174, "install-sgkit"]], "Download the data": [[174, "download-the-data"]], "Run the conversion": [[174, "run-the-conversion"]], "Inspect the dataset": [[174, "inspect-the-dataset"]]}, "indexentries": {"fst() (in module sgkit)": [[7, "sgkit.Fst"]], "garud_h() (in module sgkit)": [[8, "sgkit.Garud_H"]], "tajimas_d() (in module sgkit)": [[9, "sgkit.Tajimas_D"]], "weir_goudet_beta() (in module sgkit)": [[10, "sgkit.Weir_Goudet_beta"]], "call_allele_frequencies() (in module sgkit)": [[11, "sgkit.call_allele_frequencies"]], "cohort_allele_frequencies() (in module sgkit)": [[12, "sgkit.cohort_allele_frequencies"]], "convert_call_to_index() (in module sgkit)": [[13, "sgkit.convert_call_to_index"]], "convert_probability_to_call() (in module sgkit)": [[14, "sgkit.convert_probability_to_call"]], "count_call_alleles() (in module sgkit)": [[15, "sgkit.count_call_alleles"]], "count_cohort_alleles() (in module sgkit)": [[16, "sgkit.count_cohort_alleles"]], "count_variant_alleles() (in module sgkit)": [[17, "sgkit.count_variant_alleles"]], "count_variant_genotypes() (in module sgkit)": [[18, "sgkit.count_variant_genotypes"]], "display_genotypes() (in module sgkit)": [[19, "sgkit.display_genotypes"]], "display_pedigree() (in module sgkit)": [[20, "sgkit.display_pedigree"]], "divergence() (in module sgkit)": [[21, "sgkit.divergence"]], "diversity() (in module sgkit)": [[22, "sgkit.diversity"]], "filter_partial_calls() (in module sgkit)": [[23, "sgkit.filter_partial_calls"]], "genee() (in module sgkit)": [[24, "sgkit.genee"]], "genomic_relationship() (in module sgkit)": [[25, "sgkit.genomic_relationship"]], "gwas_linear_regression() (in module sgkit)": [[26, "sgkit.gwas_linear_regression"]], "hardy_weinberg_test() (in module sgkit)": [[27, "sgkit.hardy_weinberg_test"]], "hybrid_inverse_relationship() (in module sgkit)": [[28, "sgkit.hybrid_inverse_relationship"]], "hybrid_relationship() (in module sgkit)": [[29, "sgkit.hybrid_relationship"]], "identity_by_state() (in module sgkit)": [[30, "sgkit.identity_by_state"]], "individual_heterozygosity() (in module sgkit)": [[31, "sgkit.individual_heterozygosity"]], "infer_call_ploidy() (in module sgkit)": [[32, "sgkit.infer_call_ploidy"]], "infer_sample_ploidy() (in module sgkit)": [[33, "sgkit.infer_sample_ploidy"]], "infer_variant_ploidy() (in module sgkit)": [[34, "sgkit.infer_variant_ploidy"]], "invert_relationship_matrix() (in module sgkit)": [[35, "sgkit.invert_relationship_matrix"]], "bgen_to_zarr() (in module sgkit.io.bgen)": [[36, "sgkit.io.bgen.bgen_to_zarr"]], "read_bgen() (in module sgkit.io.bgen)": [[37, "sgkit.io.bgen.read_bgen"]], "rechunk_bgen() (in module sgkit.io.bgen)": [[38, "sgkit.io.bgen.rechunk_bgen"]], "plink_to_zarr() (in module sgkit.io.plink)": [[39, "sgkit.io.plink.plink_to_zarr"]], "read_plink() (in module sgkit.io.plink)": [[40, "sgkit.io.plink.read_plink"]], "write_plink() (in module sgkit.io.plink)": [[41, "sgkit.io.plink.write_plink"]], "zarr_to_plink() (in module sgkit.io.plink)": [[42, "sgkit.io.plink.zarr_to_plink"]], "concat_zarrs() (in module sgkit.io.vcf)": [[43, "sgkit.io.vcf.concat_zarrs"]], "partition_into_regions() (in module sgkit.io.vcf)": [[44, "sgkit.io.vcf.partition_into_regions"]], "read_vcf() (in module sgkit.io.vcf)": [[45, "sgkit.io.vcf.read_vcf"]], "vcf_to_zarr() (in module sgkit.io.vcf)": [[46, "sgkit.io.vcf.vcf_to_zarr"]], "vcf_to_zarrs() (in module sgkit.io.vcf)": [[47, "sgkit.io.vcf.vcf_to_zarrs"]], "write_vcf() (in module sgkit.io.vcf)": [[48, "sgkit.io.vcf.write_vcf"]], "zarr_array_sizes() (in module sgkit.io.vcf)": [[49, "sgkit.io.vcf.zarr_array_sizes"]], "zarr_to_vcf() (in module sgkit.io.vcf)": [[50, "sgkit.io.vcf.zarr_to_vcf"]], "ld_matrix() (in module sgkit)": [[51, "sgkit.ld_matrix"]], "ld_prune() (in module sgkit)": [[52, "sgkit.ld_prune"]], "load_dataset() (in module sgkit)": [[53, "sgkit.load_dataset"]], "maximal_independent_set() (in module sgkit)": [[54, "sgkit.maximal_independent_set"]], "observed_heterozygosity() (in module sgkit)": [[55, "sgkit.observed_heterozygosity"]], "pairwise_distance() (in module sgkit)": [[56, "sgkit.pairwise_distance"]], "parent_indices() (in module sgkit)": [[57, "sgkit.parent_indices"]], "pbs() (in module sgkit)": [[58, "sgkit.pbs"]], "pc_relate() (in module sgkit)": [[59, "sgkit.pc_relate"]], "pedigree_contribution() (in module sgkit)": [[60, "sgkit.pedigree_contribution"]], "pedigree_inbreeding() (in module sgkit)": [[61, "sgkit.pedigree_inbreeding"]], "pedigree_inverse_kinship() (in module sgkit)": [[62, "sgkit.pedigree_inverse_kinship"]], "pedigree_kinship() (in module sgkit)": [[63, "sgkit.pedigree_kinship"]], "pedigree_sel() (in module sgkit)": [[64, "sgkit.pedigree_sel"]], "read_scikit_allel_vcfzarr() (in module sgkit)": [[65, "sgkit.read_scikit_allel_vcfzarr"]], "regenie() (in module sgkit)": [[66, "sgkit.regenie"]], "sample_stats() (in module sgkit)": [[67, "sgkit.sample_stats"]], "save_dataset() (in module sgkit)": [[68, "sgkit.save_dataset"]], "simulate_genedrop() (in module sgkit)": [[69, "sgkit.simulate_genedrop"]], "simulate_genotype_call_dataset() (in module sgkit)": [[70, "sgkit.simulate_genotype_call_dataset"]], "call_allele_count_spec (in module sgkit.variables)": [[71, "sgkit.variables.call_allele_count_spec"]], "call_allele_frequency_spec (in module sgkit.variables)": [[72, "sgkit.variables.call_allele_frequency_spec"]], "call_dosage_mask_spec (in module sgkit.variables)": [[73, "sgkit.variables.call_dosage_mask_spec"]], "call_dosage_spec (in module sgkit.variables)": [[74, "sgkit.variables.call_dosage_spec"]], "call_genotype_complete_mask_spec (in module sgkit.variables)": [[75, "sgkit.variables.call_genotype_complete_mask_spec"]], "call_genotype_complete_spec (in module sgkit.variables)": [[76, "sgkit.variables.call_genotype_complete_spec"]], "call_genotype_fill_spec (in module sgkit.variables)": [[77, "sgkit.variables.call_genotype_fill_spec"]], "call_genotype_index_mask_spec (in module sgkit.variables)": [[78, "sgkit.variables.call_genotype_index_mask_spec"]], "call_genotype_index_spec (in module sgkit.variables)": [[79, "sgkit.variables.call_genotype_index_spec"]], "call_genotype_mask_spec (in module sgkit.variables)": [[80, "sgkit.variables.call_genotype_mask_spec"]], "call_genotype_phased_spec (in module sgkit.variables)": [[81, "sgkit.variables.call_genotype_phased_spec"]], "call_genotype_probability_mask_spec (in module sgkit.variables)": [[82, "sgkit.variables.call_genotype_probability_mask_spec"]], "call_genotype_probability_spec (in module sgkit.variables)": [[83, "sgkit.variables.call_genotype_probability_spec"]], "call_genotype_spec (in module sgkit.variables)": [[84, "sgkit.variables.call_genotype_spec"]], "call_heterozygosity_spec (in module sgkit.variables)": [[85, "sgkit.variables.call_heterozygosity_spec"]], "call_ploidy_spec (in module sgkit.variables)": [[86, "sgkit.variables.call_ploidy_spec"]], "cohort_allele_count_spec (in module sgkit.variables)": [[87, "sgkit.variables.cohort_allele_count_spec"]], "cohort_allele_frequency_spec (in module sgkit.variables)": [[88, "sgkit.variables.cohort_allele_frequency_spec"]], "covariates_spec (in module sgkit.variables)": [[89, "sgkit.variables.covariates_spec"]], "interval_contig_name_spec (in module sgkit.variables)": [[90, "sgkit.variables.interval_contig_name_spec"]], "interval_start_spec (in module sgkit.variables)": [[91, "sgkit.variables.interval_start_spec"]], "interval_stop_spec (in module sgkit.variables)": [[92, "sgkit.variables.interval_stop_spec"]], "ld_prune_index_to_drop_spec (in module sgkit.variables)": [[93, "sgkit.variables.ld_prune_index_to_drop_spec"]], "parent_id_spec (in module sgkit.variables)": [[94, "sgkit.variables.parent_id_spec"]], "parent_spec (in module sgkit.variables)": [[95, "sgkit.variables.parent_spec"]], "pc_relate_phi_spec (in module sgkit.variables)": [[96, "sgkit.variables.pc_relate_phi_spec"]], "regenie_base_prediction_spec (in module sgkit.variables)": [[97, "sgkit.variables.regenie_base_prediction_spec"]], "regenie_loco_prediction_spec (in module sgkit.variables)": [[98, "sgkit.variables.regenie_loco_prediction_spec"]], "regenie_meta_prediction_spec (in module sgkit.variables)": [[99, "sgkit.variables.regenie_meta_prediction_spec"]], "sample_call_rate_spec (in module sgkit.variables)": [[100, "sgkit.variables.sample_call_rate_spec"]], "sample_cohort_spec (in module sgkit.variables)": [[101, "sgkit.variables.sample_cohort_spec"]], "sample_id_spec (in module sgkit.variables)": [[102, "sgkit.variables.sample_id_spec"]], "sample_n_called_spec (in module sgkit.variables)": [[103, "sgkit.variables.sample_n_called_spec"]], "sample_n_het_spec (in module sgkit.variables)": [[104, "sgkit.variables.sample_n_het_spec"]], "sample_n_hom_alt_spec (in module sgkit.variables)": [[105, "sgkit.variables.sample_n_hom_alt_spec"]], "sample_n_hom_ref_spec (in module sgkit.variables)": [[106, "sgkit.variables.sample_n_hom_ref_spec"]], "sample_n_non_ref_spec (in module sgkit.variables)": [[107, "sgkit.variables.sample_n_non_ref_spec"]], "sample_pca_component_spec (in module sgkit.variables)": [[108, "sgkit.variables.sample_pca_component_spec"]], "sample_pca_explained_variance_ratio_spec (in module sgkit.variables)": [[109, "sgkit.variables.sample_pca_explained_variance_ratio_spec"]], "sample_pca_explained_variance_spec (in module sgkit.variables)": [[110, "sgkit.variables.sample_pca_explained_variance_spec"]], "sample_pca_loading_spec (in module sgkit.variables)": [[111, "sgkit.variables.sample_pca_loading_spec"]], "sample_pca_projection_spec (in module sgkit.variables)": [[112, "sgkit.variables.sample_pca_projection_spec"]], "sample_ploidy_spec (in module sgkit.variables)": [[113, "sgkit.variables.sample_ploidy_spec"]], "stat_fst_spec (in module sgkit.variables)": [[114, "sgkit.variables.stat_Fst_spec"]], "stat_garud_h123_spec (in module sgkit.variables)": [[115, "sgkit.variables.stat_Garud_h123_spec"]], "stat_garud_h12_spec (in module sgkit.variables)": [[116, "sgkit.variables.stat_Garud_h12_spec"]], "stat_garud_h1_spec (in module sgkit.variables)": [[117, "sgkit.variables.stat_Garud_h1_spec"]], "stat_garud_h2_h1_spec (in module sgkit.variables)": [[118, "sgkit.variables.stat_Garud_h2_h1_spec"]], "stat_hamilton_kerr_lambda_spec (in module sgkit.variables)": [[119, "sgkit.variables.stat_Hamilton_Kerr_lambda_spec"]], "stat_hamilton_kerr_tau_spec (in module sgkit.variables)": [[120, "sgkit.variables.stat_Hamilton_Kerr_tau_spec"]], "stat_tajimas_d_spec (in module sgkit.variables)": [[121, "sgkit.variables.stat_Tajimas_D_spec"]], "stat_weir_goudet_beta_spec (in module sgkit.variables)": [[122, "sgkit.variables.stat_Weir_Goudet_beta_spec"]], "stat_divergence_spec (in module sgkit.variables)": [[123, "sgkit.variables.stat_divergence_spec"]], "stat_diversity_spec (in module sgkit.variables)": [[124, "sgkit.variables.stat_diversity_spec"]], "stat_genomic_kinship_spec (in module sgkit.variables)": [[125, "sgkit.variables.stat_genomic_kinship_spec"]], "stat_genomic_relationship_spec (in module sgkit.variables)": [[126, "sgkit.variables.stat_genomic_relationship_spec"]], "stat_hybrid_inverse_relationship_spec (in module sgkit.variables)": [[127, "sgkit.variables.stat_hybrid_inverse_relationship_spec"]], "stat_hybrid_relationship_spec (in module sgkit.variables)": [[128, "sgkit.variables.stat_hybrid_relationship_spec"]], "stat_identity_by_state_spec (in module sgkit.variables)": [[129, "sgkit.variables.stat_identity_by_state_spec"]], "stat_inverse_relationship_spec (in module sgkit.variables)": [[130, "sgkit.variables.stat_inverse_relationship_spec"]], "stat_observed_heterozygosity_spec (in module sgkit.variables)": [[131, "sgkit.variables.stat_observed_heterozygosity_spec"]], "stat_pbs_spec (in module sgkit.variables)": [[132, "sgkit.variables.stat_pbs_spec"]], "stat_pedigree_contribution_spec (in module sgkit.variables)": [[133, "sgkit.variables.stat_pedigree_contribution_spec"]], "stat_pedigree_inbreeding_spec (in module sgkit.variables)": [[134, "sgkit.variables.stat_pedigree_inbreeding_spec"]], "stat_pedigree_inverse_kinship_spec (in module sgkit.variables)": [[135, "sgkit.variables.stat_pedigree_inverse_kinship_spec"]], "stat_pedigree_inverse_relationship_spec (in module sgkit.variables)": [[136, "sgkit.variables.stat_pedigree_inverse_relationship_spec"]], "stat_pedigree_kinship_spec (in module sgkit.variables)": [[137, "sgkit.variables.stat_pedigree_kinship_spec"]], "stat_pedigree_relationship_spec (in module sgkit.variables)": [[138, "sgkit.variables.stat_pedigree_relationship_spec"]], "traits_spec (in module sgkit.variables)": [[139, "sgkit.variables.traits_spec"]], "variant_allele_count_spec (in module sgkit.variables)": [[140, "sgkit.variables.variant_allele_count_spec"]], "variant_allele_frequency_spec (in module sgkit.variables)": [[141, "sgkit.variables.variant_allele_frequency_spec"]], "variant_allele_spec (in module sgkit.variables)": [[142, "sgkit.variables.variant_allele_spec"]], "variant_allele_total_spec (in module sgkit.variables)": [[143, "sgkit.variables.variant_allele_total_spec"]], "variant_call_rate_spec (in module sgkit.variables)": [[144, "sgkit.variables.variant_call_rate_spec"]], "variant_contig_spec (in module sgkit.variables)": [[145, "sgkit.variables.variant_contig_spec"]], "variant_genotype_count_spec (in module sgkit.variables)": [[146, "sgkit.variables.variant_genotype_count_spec"]], "variant_hwe_p_value_spec (in module sgkit.variables)": [[147, "sgkit.variables.variant_hwe_p_value_spec"]], "variant_id_spec (in module sgkit.variables)": [[148, "sgkit.variables.variant_id_spec"]], "variant_linreg_beta_spec (in module sgkit.variables)": [[149, "sgkit.variables.variant_linreg_beta_spec"]], "variant_linreg_p_value_spec (in module sgkit.variables)": [[150, "sgkit.variables.variant_linreg_p_value_spec"]], "variant_linreg_t_value_spec (in module sgkit.variables)": [[151, "sgkit.variables.variant_linreg_t_value_spec"]], "variant_n_called_spec (in module sgkit.variables)": [[152, "sgkit.variables.variant_n_called_spec"]], "variant_n_het_spec (in module sgkit.variables)": [[153, "sgkit.variables.variant_n_het_spec"]], "variant_n_hom_alt_spec (in module sgkit.variables)": [[154, "sgkit.variables.variant_n_hom_alt_spec"]], "variant_n_hom_ref_spec (in module sgkit.variables)": [[155, "sgkit.variables.variant_n_hom_ref_spec"]], "variant_n_non_ref_spec (in module sgkit.variables)": [[156, "sgkit.variables.variant_n_non_ref_spec"]], "variant_ploidy_spec (in module sgkit.variables)": [[157, "sgkit.variables.variant_ploidy_spec"]], "variant_position_spec (in module sgkit.variables)": [[158, "sgkit.variables.variant_position_spec"]], "variant_score_spec (in module sgkit.variables)": [[159, "sgkit.variables.variant_score_spec"]], "window_contig_spec (in module sgkit.variables)": [[160, "sgkit.variables.window_contig_spec"]], "window_start_spec (in module sgkit.variables)": [[161, "sgkit.variables.window_start_spec"]], "window_stop_spec (in module sgkit.variables)": [[162, "sgkit.variables.window_stop_spec"]], "variant_stats() (in module sgkit)": [[163, "sgkit.variant_stats"]], "window_by_genome() (in module sgkit)": [[164, "sgkit.window_by_genome"]], "window_by_interval() (in module sgkit)": [[165, "sgkit.window_by_interval"]], "window_by_position() (in module sgkit)": [[166, "sgkit.window_by_position"]], "window_by_variant() (in module sgkit)": [[167, "sgkit.window_by_variant"]]}})
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diff --git a/latest/user_guide.html b/latest/user_guide.html
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--- a/latest/user_guide.html
+++ b/latest/user_guide.html
@@ -1081,8 +1081,8 @@ <h3><a class="toc-backref" href="#id25" role="doc-backlink">Monitoring operation
 <span class="gp">   ....: </span>    <span class="n">ac</span> <span class="o">=</span> <span class="n">sg</span><span class="o">.</span><span class="n">count_variant_alleles</span><span class="p">(</span><span class="n">ds</span><span class="p">)</span><span class="o">.</span><span class="n">variant_allele_count</span><span class="o">.</span><span class="n">compute</span><span class="p">()</span>
 <span class="gp">   ....: </span>
 
-<span class="go">[                                        ] | 0% Completed | 190.27 us</span>
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+<span class="go">[                                        ] | 0% Completed | 162.42 us</span>
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 <span class="gp">In [39]: </span><span class="n">ac</span><span class="p">[:</span><span class="mi">5</span><span class="p">]</span>
 <span class="gh">Out[39]: </span>