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@brentp brentp released this 31 Jan 12:38
· 80 commits to main since this release
v0.1.1
3fd15aa

This release adds the ability to annotate with multiple echtvar files and to annotate with string fields, including support for extracting the FILTER field. Here is the changelog:

v0.1.1

  • support multiple echtvar files to echtvar anno. This makes it possible to annoate with, for example gnomad and dbsnp.
  • support string fields. This works for fields with a lowish number (max of thousands) of unique values.
  • support extracting FILTER field from annotation VCF. So now can annotate with, e.g. gnomad FILTER field via: 
    {"field": "FILTER", "alias": "gnomad_filter"},
    in the json file for echtvar encode. "FILTER" is a special-case, all other fields are from the INFO.

⚠️ echtvar requires a precessor that supports SSE4.1 instructions. Using echtvar on an unsupported processor will result in a SIGILL.

Get Started

To get started, either download the static linux binary here, then chmod +x and execute; or use cargo build

Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download
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