From 308d147a374c8d68d3a3ea32fa2325b3a479f27e Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Wed, 25 Sep 2024 18:24:38 +0200 Subject: [PATCH 1/8] wip --- .github/workflows/ci.yml | 1 + CHANGELOG.md | 1 + assets/svdb_query_vcf_schema.json | 40 +++++ conf/modules/annotate_svs.config | 57 +++++++ conf/modules/call_svs.config | 2 +- conf/modules/snv_annotation.config | 2 +- conf/test.config | 3 +- modules.json | 10 ++ modules/nf-core/svdb/build/environment.yml | 5 + modules/nf-core/svdb/build/main.nf | 48 ++++++ modules/nf-core/svdb/build/meta.yml | 38 +++++ modules/nf-core/svdb/build/tests/main.nf.test | 111 ++++++++++++ .../svdb/build/tests/main.nf.test.snap | 94 +++++++++++ modules/nf-core/svdb/build/tests/tags.yml | 2 + modules/nf-core/svdb/query/environment.yml | 5 + modules/nf-core/svdb/query/main.nf | 77 +++++++++ modules/nf-core/svdb/query/meta.yml | 63 +++++++ modules/nf-core/svdb/query/tests/main.nf.test | 36 ++++ .../svdb/query/tests/main.nf.test.snap | 30 ++++ modules/nf-core/svdb/query/tests/tags.yml | 2 + nextflow.config | 3 + nextflow_schema.json | 16 ++ subworkflows/local/annotate_svs/main.nf | 61 +++++++ .../local/annotate_svs/tests/main.nf.test | 90 ++++++++++ .../annotate_svs/tests/main.nf.test.snap | 158 ++++++++++++++++++ .../local/annotate_svs/tests/nextflow.config | 14 ++ subworkflows/local/snv_annotation/main.nf | 16 +- .../snv_annotation/tests/nextflow.config | 2 +- .../local/utils_nfcore_nallo_pipeline/main.nf | 5 + tests/main.nf.test | 18 +- workflows/nallo.nf | 18 ++ 31 files changed, 1007 insertions(+), 21 deletions(-) create mode 100644 assets/svdb_query_vcf_schema.json create mode 100644 conf/modules/annotate_svs.config create mode 100644 modules/nf-core/svdb/build/environment.yml create mode 100644 modules/nf-core/svdb/build/main.nf create mode 100644 modules/nf-core/svdb/build/meta.yml create mode 100644 modules/nf-core/svdb/build/tests/main.nf.test create mode 100644 modules/nf-core/svdb/build/tests/main.nf.test.snap create mode 100644 modules/nf-core/svdb/build/tests/tags.yml create mode 100644 modules/nf-core/svdb/query/environment.yml create mode 100644 modules/nf-core/svdb/query/main.nf create mode 100644 modules/nf-core/svdb/query/meta.yml create mode 100644 modules/nf-core/svdb/query/tests/main.nf.test create mode 100644 modules/nf-core/svdb/query/tests/main.nf.test.snap create mode 100644 modules/nf-core/svdb/query/tests/tags.yml create mode 100644 subworkflows/local/annotate_svs/main.nf create mode 100644 subworkflows/local/annotate_svs/tests/main.nf.test create mode 100644 subworkflows/local/annotate_svs/tests/main.nf.test.snap create mode 100644 subworkflows/local/annotate_svs/tests/nextflow.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f6ba16cb..c512f454 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -37,6 +37,7 @@ jobs: - "SHORT_VARIANT_CALLING" - "SNV_ANNOTATION" - "CALL_SVS" + - "ANNOTATE_SVS" profile: - "docker" diff --git a/CHANGELOG.md b/CHANGELOG.md index a6a32a52..399c8645 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#388](https://github.com/genomic-medicine-sweden/nallo/pull/388) - Added single-sample tbi output to the short variant calling subworkflow - [#393](https://github.com/genomic-medicine-sweden/nallo/pull/393) - Added a new `--minimap2_read_mapping_preset` parameter - [#403](https://github.com/genomic-medicine-sweden/nallo/pull/403) - Added `FOUND_IN=hificnv` tags to CNV calling output +- [#408](https://github.com/genomic-medicine-sweden/nallo/pull/408) - Added a new subworkflow to annotate SVs - [#417](https://github.com/genomic-medicine-sweden/nallo/pull/417) - Added `FOUND_IN=deepvariant` tags to SNV calling output ### `Changed` diff --git a/assets/svdb_query_vcf_schema.json b/assets/svdb_query_vcf_schema.json new file mode 100644 index 00000000..0bb8540a --- /dev/null +++ b/assets/svdb_query_vcf_schema.json @@ -0,0 +1,40 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json", + "title": "Schema for SVDB query - VCF", + "description": "Schema for the SVDB query database input, VCF version", + "type": "array", + "items": { + "type": "object", + "properties": { + "filename": { + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.vcf?(\\.gz)?$", + "errorMessage": "Path to query database cannot contain spaces and must be a vcf file" + }, + "in_freq_info_key": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "In frequency key cannot contain spaces" + }, + "in_allele_count_info_key": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "In allele count key cannot contain spaces" + }, + "out_freq_info_key": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Out frequency key must be provided and cannot contain spaces" + }, + "out_allele_count_info_key": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Out allele count key must be provided and cannot contain spaces" + } + }, + "required": ["filename", "out_freq_info_key", "out_allele_count_info_key"] + } +} diff --git a/conf/modules/annotate_svs.config b/conf/modules/annotate_svs.config new file mode 100644 index 00000000..4e2d31c6 --- /dev/null +++ b/conf/modules/annotate_svs.config @@ -0,0 +1,57 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. +---------------------------------------------------------------------------------------- +*/ + +process { + + /* + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Annotate SVs + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + */ + + withName: '.*:ANNOTATE_SVS:.*' { + publishDir = [ + enabled: false, + ] + } + + withName: '.*ANNOTATE_SVS:ENSEMBLVEP_SV' { + ext.args = { [ + "${params.extra_vep_options}", + "--dir_plugins .", + '--plugin pLI,pLI_values.txt', + '--appris --biotype --buffer_size 100 --canonical --cache --ccds', + '--compress_output bgzip --distance 5000 --domains', + '--exclude_predicted --force_overwrite --format vcf', + '--fork 4 --hgvs --humdiv --max_sv_size 248387328', + '--no_progress --numbers --per_gene --polyphen p', + '--protein --offline --sift p', // Add back regulatory with VEP 113 + '--symbol --tsl --uniprot --vcf', + '--no_stats' + ].join(' ') } + ext.prefix = { "${meta.id}_svs_annotated" } + publishDir = [ + path: { "${params.outdir}/svs/multi_sample/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*ANNOTATE_SVS:TABIX_VEP' { + publishDir = [ + path: { "${params.outdir}/svs/multi_sample/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + +} diff --git a/conf/modules/call_svs.config b/conf/modules/call_svs.config index 842df531..c5fdabe0 100644 --- a/conf/modules/call_svs.config +++ b/conf/modules/call_svs.config @@ -57,7 +57,7 @@ process { publishDir = [ path: { "${params.outdir}/svs/multi_sample/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + saveAs: { filename -> filename.equals('versions.yml') || params.skip_sv_annotation ? null : filename } ] } diff --git a/conf/modules/snv_annotation.config b/conf/modules/snv_annotation.config index 9f2b393d..ec2063b3 100644 --- a/conf/modules/snv_annotation.config +++ b/conf/modules/snv_annotation.config @@ -36,7 +36,7 @@ process { ].join(' ') } - withName: '.*:SNV_ANNOTATION:ENSEMBLVEP_VEP' { + withName: '.*:SNV_ANNOTATION:ENSEMBLVEP_SNV' { ext.prefix = { "${meta.id}_vep" } ext.args = { [ "${params.extra_vep_options}", diff --git a/conf/test.config b/conf/test.config index 1e01f42d..7f095770 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,7 +26,7 @@ params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' // Base directory for genomic-medicine-sweden/nallo test data - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/' // References fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz' @@ -41,6 +41,7 @@ params { vep_cache = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz' vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv' snp_db = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv' + svdb_dbs = params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv' reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv' score_config_snv = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini' variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' diff --git a/modules.json b/modules.json index 4c1ac8e5..39279d5d 100644 --- a/modules.json +++ b/modules.json @@ -244,6 +244,16 @@ "git_sha": "4806239588f35d27a95b187b4000d80e15152022", "installed_by": ["modules"] }, + "svdb/build": { + "branch": "master", + "git_sha": "ba8aac9d0b2f34811800bafab168b638cf2ff3cc", + "installed_by": ["modules"] + }, + "svdb/query": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, "tabix/bgzip": { "branch": "master", "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", diff --git a/modules/nf-core/svdb/build/environment.yml b/modules/nf-core/svdb/build/environment.yml new file mode 100644 index 00000000..cd35cf48 --- /dev/null +++ b/modules/nf-core/svdb/build/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::svdb=2.8.1 diff --git a/modules/nf-core/svdb/build/main.nf b/modules/nf-core/svdb/build/main.nf new file mode 100644 index 00000000..db3055e2 --- /dev/null +++ b/modules/nf-core/svdb/build/main.nf @@ -0,0 +1,48 @@ +process SVDB_BUILD { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/svdb:2.8.1--py39h5371cbf_0': + 'biocontainers/svdb:2.8.1--py39h5371cbf_0' }" + + input: + tuple val(meta), path(input) + val(input_type) + + output: + tuple val(meta), path("*.db"), emit: db + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if (!input_type.matches('folder|files')) { error "Unrecognised input type. Options are: 'folder', 'files'" } + + """ + svdb \\ + --build \\ + --$input_type $input \\ + --prefix ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.db + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/svdb/build/meta.yml b/modules/nf-core/svdb/build/meta.yml new file mode 100644 index 00000000..c5c5a992 --- /dev/null +++ b/modules/nf-core/svdb/build/meta.yml @@ -0,0 +1,38 @@ +name: svdb_build +description: Build a structural variant database +keywords: + - structural variants + - build + - svdb +tools: + - svdb: + description: structural variant database software + homepage: https://github.com/J35P312/SVDB + documentation: https://github.com/J35P312/SVDB/blob/master/README.md + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input VCF file(s) or folder + pattern: "*" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - db: + type: file + description: SVDB database +authors: + - "@fellen31" diff --git a/modules/nf-core/svdb/build/tests/main.nf.test b/modules/nf-core/svdb/build/tests/main.nf.test new file mode 100644 index 00000000..ccf18f2b --- /dev/null +++ b/modules/nf-core/svdb/build/tests/main.nf.test @@ -0,0 +1,111 @@ +nextflow_process { + + name "Test Process SVDB_BUILD" + script "modules/nf-core/svdb/build/main.nf" + process "SVDB_BUILD" + tag "modules" + tag "modules_nfcore" + tag "svdb" + tag "svdb/build" + + test("one VCF - files") { + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] + ]) + input[1] = 'files' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.db.get(0).get(1)).name, + process.out.versions + ).match() } + ) + } + } + + test("two VCFs - files") { + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true) + ] + ]) + input[1] = 'files' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.db.get(0).get(1)).name, + process.out.versions + ).match() } + ) + } + } + + test("one VCF - files -stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] + ]) + input[1] = 'files' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("two VCFs - files -stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true) + ] + ]) + input[1] = 'files' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/svdb/build/tests/main.nf.test.snap b/modules/nf-core/svdb/build/tests/main.nf.test.snap new file mode 100644 index 00000000..9a992957 --- /dev/null +++ b/modules/nf-core/svdb/build/tests/main.nf.test.snap @@ -0,0 +1,94 @@ +{ + "one VCF - files": { + "content": [ + "test.db", + [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T11:37:21.374511177" + }, + "two VCFs - files": { + "content": [ + "test.db", + [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T11:37:27.968892336" + }, + "two VCFs - files -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ], + "db": [ + [ + { + "id": "test" + }, + "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T11:40:04.558825564" + }, + "one VCF - files -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ], + "db": [ + [ + { + "id": "test" + }, + "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T10:54:45.735248435" + } +} \ No newline at end of file diff --git a/modules/nf-core/svdb/build/tests/tags.yml b/modules/nf-core/svdb/build/tests/tags.yml new file mode 100644 index 00000000..7eb9b2ab --- /dev/null +++ b/modules/nf-core/svdb/build/tests/tags.yml @@ -0,0 +1,2 @@ +svdb/query: + - modules/nf-core/svdb/build/** diff --git a/modules/nf-core/svdb/query/environment.yml b/modules/nf-core/svdb/query/environment.yml new file mode 100644 index 00000000..cd35cf48 --- /dev/null +++ b/modules/nf-core/svdb/query/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::svdb=2.8.1 diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf new file mode 100644 index 00000000..d516d382 --- /dev/null +++ b/modules/nf-core/svdb/query/main.nf @@ -0,0 +1,77 @@ +process SVDB_QUERY { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/svdb:2.8.1--py39h5371cbf_0': + 'biocontainers/svdb:2.8.1--py39h5371cbf_0' }" + + input: + tuple val(meta), path(vcf) + val(in_occs) + val(in_frqs) + val(out_occs) + val(out_frqs) + path(vcf_dbs) + path(bedpe_dbs) + + output: + tuple val(meta), path("*_query.vcf") , emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def in_occ = "" + def in_frq = "" + def out_occ = "" + def out_frq = "" + def dbs_argument = vcf_dbs ? "--db ${vcf_dbs.join(',')}" : '' + def bedpeds_argument = bedpe_dbs ? "--bedpedb ${bedpe_dbs.join(',')}" : '' + if (in_occs) { + in_occ = "--in_occ ${in_occs.join(',')}" + } + if (in_frqs) { + in_frq = "--in_frq ${in_frqs.join(',')}" + } + if (out_occs) { + out_occ = "--out_occ ${out_occs.join(',')}" + } + if (out_frqs) { + out_frq = "--out_frq ${out_frqs.join(',')}" + } + if ( vcf_dbs && bedpe_dbs ) error "bedpedb input is not compatible with db inputs" + """ + svdb \\ + --query \\ + $in_occ \\ + $in_frq \\ + $out_occ \\ + $out_frq \\ + $args \\ + $dbs_argument \\ + $bedpeds_argument \\ + --query_vcf $vcf \\ + --prefix ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_query.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/svdb/query/meta.yml b/modules/nf-core/svdb/query/meta.yml new file mode 100644 index 00000000..f8cd33c8 --- /dev/null +++ b/modules/nf-core/svdb/query/meta.yml @@ -0,0 +1,63 @@ +name: svdb_query +description: Query a structural variant database, using a vcf file as query +keywords: + - structural variants + - query + - svdb +tools: + - svdb: + description: structural variant database software + homepage: https://github.com/J35P312/SVDB + documentation: https://github.com/J35P312/SVDB/blob/master/README.md + licence: ["MIT"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: query vcf file + pattern: "*.{vcf,vcf.gz}" + - - in_occs: + type: list + description: A list of allele count tags + - - in_frqs: + type: list + description: A list of allele frequency tags + - - out_occs: + type: list + description: A list of allele count tags + - - out_frqs: + type: list + description: A list of allele frequency tags + - - vcf_dbs: + type: file + description: path to a database vcf, or a comma separated list of vcfs + pattern: "*.{vcf,vcf.gz}" + - - bedpe_dbs: + type: file + description: path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, + or a comma separated list of files + pattern: "*.{bedpe}" +output: + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_query.vcf": + type: file + description: Annotated output VCF file + pattern: "*_query.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@ramprasadn" diff --git a/modules/nf-core/svdb/query/tests/main.nf.test b/modules/nf-core/svdb/query/tests/main.nf.test new file mode 100644 index 00000000..72e82915 --- /dev/null +++ b/modules/nf-core/svdb/query/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SVDB_QUERY" + script "modules/nf-core/svdb/query/main.nf" + process "SVDB_QUERY" + tag "modules" + tag "modules_nfcore" + tag "svdb" + tag "svdb/query" + + test("svdb query") { + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] + ]) + input[1] = ['AC'] + input[2] = ['AF'] + input[3] = ['gnomad_svAC'] + input[4] = ['gnomad_svAF'] + input[5] = Channel.of([file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz', checkIfExists: true)]) + input[6] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(file(process.out.vcf[0][1]).name, file(process.out.versions[0]).name).match()} + ) + } + } +} diff --git a/modules/nf-core/svdb/query/tests/main.nf.test.snap b/modules/nf-core/svdb/query/tests/main.nf.test.snap new file mode 100644 index 00000000..22021d0a --- /dev/null +++ b/modules/nf-core/svdb/query/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + "svdb query": { + "content": [ + "test_query.vcf", + "versions.yml" + ], + "timestamp": "2023-11-22T14:56:08.90223505" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,e10873514a6dfc4ff377d645e7b3c9f5" + ] + ], + "timestamp": "2023-11-22T14:36:48.543666873" + }, + "vcf": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_query.vcf:md5,a29542606323b2430ec52ffb5c4c7f5e" + ] + ] + ], + "timestamp": "2023-11-22T14:36:48.523155905" + } +} \ No newline at end of file diff --git a/modules/nf-core/svdb/query/tests/tags.yml b/modules/nf-core/svdb/query/tests/tags.yml new file mode 100644 index 00000000..f4096378 --- /dev/null +++ b/modules/nf-core/svdb/query/tests/tags.yml @@ -0,0 +1,2 @@ +svdb/query: + - modules/nf-core/svdb/query/** diff --git a/nextflow.config b/nextflow.config index dd675f3c..d4fae7cf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -21,6 +21,7 @@ params { reduced_penetrance = null score_config_snv = null snp_db = null + svdb_dbs = null variant_consequences_snv = null vep_cache = null vep_plugin_files = null @@ -42,6 +43,7 @@ params { skip_repeat_annotation = params.preset == 'ONT_R10' ? true : false skip_short_variant_calling = false skip_snv_annotation = false + skip_sv_annotation = false deepvariant_model_type = params.preset == 'ONT_R10' ? 'ONT_R104' : 'PACBIO' minimap2_read_mapping_preset = params.preset == 'ONT_R10' ? 'lr:hq' : 'lr:hqae' @@ -313,6 +315,7 @@ includeConfig 'conf/base.config' includeConfig 'conf/modules/annotate_cadd.config' includeConfig 'conf/modules/annotate_consequence_pli.config' includeConfig 'conf/modules/annotate_repeat_expansions.config' +includeConfig 'conf/modules/annotate_svs.config' includeConfig 'conf/modules/general.config' includeConfig 'conf/modules/bam_infer_sex.config' includeConfig 'conf/modules/call_paralogs.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index f715de68..6d155698 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -64,6 +64,11 @@ "description": "Skip short variant annotation", "default": false }, + "skip_sv_annotation": { + "type": "boolean", + "description": "Skip structural variant annotation", + "default": false + }, "skip_cnv_calling": { "type": "boolean", "description": "Skip CNV calling", @@ -162,6 +167,17 @@ "description": "A csv file with echtvar databases to annotate SNVs with", "exists": true }, + "svdb_dbs": { + "type": "string", + "exists": true, + "format": "file-path", + "description": "Databases used for structural variant annotation in vcf format.", + "fa_icon": "fas fa-file-csv", + "help_text": "Path to comma-separated file containing information about the databases used for structural variant annotation.", + "pattern": "^\\S+\\.csv$", + "mimetype": "text/csv", + "schema": "assets/svdb_query_vcf_schema.json" + }, "variant_catalog": { "type": "string", "description": "A variant catalog json-file for stranger", diff --git a/subworkflows/local/annotate_svs/main.nf b/subworkflows/local/annotate_svs/main.nf new file mode 100644 index 00000000..022f523f --- /dev/null +++ b/subworkflows/local/annotate_svs/main.nf @@ -0,0 +1,61 @@ +include { SVDB_QUERY } from '../../../modules/nf-core/svdb/query/main' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_SV } from '../../../modules/nf-core/ensemblvep/vep/main' +include { TABIX_TABIX as TABIX_ENSEMBLVEP_SV } from '../../../modules/nf-core/tabix/tabix/main' + +workflow ANNOTATE_SVS { + + take: + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_sv_dbs // channel: [mandatory] [ val(meta), path(csv) ] + ch_vep_cache // channel: [mandatory] [ path(cache) ] + val_vep_cache_version // string: [mandatory] default: 110 + ch_vep_extra_files // channel: [mandatory] [ path(files) ] + + main: + ch_versions = Channel.empty() + + ch_sv_dbs + .map { meta, csv -> csv } + .splitCsv ( header:true ) + .multiMap { row -> + vcf_dbs: row.filename + in_frqs: row.in_freq_info_key + in_occs: row.in_allele_count_info_key + out_frqs: row.out_freq_info_key + out_occs: row.out_allele_count_info_key + } + .set { ch_svdb_in } + + // Annotate with SVDB VCF "databases" + SVDB_QUERY ( + ch_vcf, + ch_svdb_in.in_occs.toList(), + ch_svdb_in.in_frqs.toList(), + ch_svdb_in.out_occs.toList(), + ch_svdb_in.out_frqs.toList(), + ch_svdb_in.vcf_dbs.toList(), + [] + ) + + ENSEMBLVEP_SV ( + SVDB_QUERY.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] }, + "GRCh38", + "homo_sapiens", + val_vep_cache_version, + ch_vep_cache, + ch_fasta, + ch_vep_extra_files + ) + ch_versions = ch_versions.mix(ENSEMBLVEP_SV.out.versions) + + TABIX_ENSEMBLVEP_SV ( + ENSEMBLVEP_SV.out.vcf + ) + ch_versions = ch_versions.mix(TABIX_ENSEMBLVEP_SV.out.versions) + + emit: + vcf = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] + tbi = TABIX_ENSEMBLVEP_SV.out.tbi // channel: [ val(meta), path(tbi) ] + versions = ch_versions // channel: [ path(versions.yml) ] +} diff --git a/subworkflows/local/annotate_svs/tests/main.nf.test b/subworkflows/local/annotate_svs/tests/main.nf.test new file mode 100644 index 00000000..c480ff89 --- /dev/null +++ b/subworkflows/local/annotate_svs/tests/main.nf.test @@ -0,0 +1,90 @@ +nextflow_workflow { + + name "Test Workflow ANNOTATE_SVS" + script "../" + workflow "ANNOTATE_SVS" + config "./nextflow.config" + + setup { + run("GUNZIP") { + script "../../../../modules/nf-core/gunzip/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], + file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true) + ] + """ + } + } + + run("SAMTOOLS_FAIDX") { + script "../../../../modules/nf-core/samtools/faidx/main.nf" + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = [[],[]] + """ + } + } + + run("SEVERUS") { + script "../../../../modules/nf-core/severus/main" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false, project: 'project' ], // meta map + file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true) + )] + input[1] = [[],[]] + """ + } + } + + run("UNTAR") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ id: 'vep_cache' ], + file(params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz', checkIfExists:true) + ] + """ + } + } + + } + + test("severus, fasta, svdb, vep_cache, '110', vep_plugins") { + + when { + workflow { + """ + input[0] = SEVERUS.out.vcf + input[1] = GUNZIP.out.gunzip + input[2] = Channel.of([ + file(params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv', checkIfExists: true) + ]) + input[4] = UNTAR.out.untar.map { meta, cache -> cache } + input[5] = Channel.value('110') + input[6] = [ + file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.versions, + path(workflow.out.vcf.get(0).get(1)), + file(workflow.out.tbi.get(0).get(1)).name + ).match() } + ) + } + + } +} diff --git a/subworkflows/local/annotate_svs/tests/main.nf.test.snap b/subworkflows/local/annotate_svs/tests/main.nf.test.snap new file mode 100644 index 00000000..2b09646f --- /dev/null +++ b/subworkflows/local/annotate_svs/tests/main.nf.test.snap @@ -0,0 +1,158 @@ +{ + "bcf, db, vep_cache, '110', -stub": { + "content": [ + [ + "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22", + "versions.yml:md5,992301857689684643c42695c032a7f2", + "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", + "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" + ], + [ + [ + { + "id": "test_data.bed", + "project": null, + "contains_affected": false + }, + "test_data.bed.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "test_data.bed", + "project": null, + "contains_affected": false + }, + "test_data.bed.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-19T10:33:26.596869783" + }, + "bcf, db, vep_cache, '110'": { + "content": [ + [ + "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22", + "versions.yml:md5,992301857689684643c42695c032a7f2", + "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", + "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" + ], + "test_data.bed.vcf.gz.tbi", + [ + "##INFO=", + "##VEP-command-line='vep --assembly GRCh38 --cache --cache_version 110 --compress_output bgzip --database 0 --dir_cache [PATH]/vep_cache --fasta hg38.test.fa --fork 2 --input_file test_data.bed_filltags_anno.vcf.gz --offline --output_file test_data.bed.vcf.gz --vcf'", + "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest", + "chr16\t63972\tchr16_63972_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000262316|protein_coding||3/17||||||||||-1||HGNC|HGNC:20561,C|intron_variant&NMD_transcript_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000417043|nonsense_mediated_decay||2/3||||||||||-1||HGNC|HGNC:20561,C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000419764|protein_coding||3/3||||||||||-1|cds_end_NF|HGNC|HGNC:20561,C|intron_variant&NMD_transcript_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000428730|nonsense_mediated_decay||2/16||||||||||-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000448893|protein_coding|||||||||||4210|-1|cds_start_NF|HGNC|HGNC:20561,C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000450643|protein_coding||3/4||||||||||-1|cds_end_NF|HGNC|HGNC:20561,C|downstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000472390|retained_intron|||||||||||580|-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000482904|retained_intron|||||||||||1766|-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000486045|retained_intron|||||||||||3779|-1||HGNC|HGNC:20561,C|non_coding_transcript_exon_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000487201|retained_intron|2/3||||1177|||||||-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000493647|retained_intron|||||||||||3292|-1||HGNC|HGNC:20561\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:11:20,11,0:..", + "chr16\t86889\tchr16_86889_T_C\tT\tC\t21\t.\tAF=1;AQ=21;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000219431|protein_coding|||||||||||1047|1||HGNC|HGNC:7211,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000356432|protein_coding|||||||||||1043|1||HGNC|HGNC:7211,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000397817|protein_coding|||||||||||1038|1||HGNC|HGNC:7211,C|intron_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000399953|protein_coding||11/11||||||||||-1||HGNC|HGNC:14124,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000436333|protein_coding|||||||||||1205|1|cds_end_NF|HGNC|HGNC:7211,C|upstream_gene_variant|MODIFIER||ENSG00000269482|Transcript|ENST00000601483|lncRNA|||||||||||3742|1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000610509|retained_intron||1/2||||||||||-1||HGNC|HGNC:14124,C|intron_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000611875|protein_coding||13/13||||||||||-1||HGNC|HGNC:14124,C|intron_variant&NMD_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000621703|nonsense_mediated_decay||10/10||||||||||-1||HGNC|HGNC:14124,C|intron_variant&NMD_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000622194|nonsense_mediated_decay||11/11||||||||||-1||HGNC|HGNC:14124\tGT:DP:AD:GQ:PL:RNC\t1/1:28:0,28:18:21,20,0:..", + "chr16\t160055\tchr16_160055_C_G\tC\tG\t18\t.\tAF=1;AQ=18;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3067|1||HGNC|HGNC:4836,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4427|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,29:17:18,22,0:..", + "chr16\t160070\tchr16_160070_C_CGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\tC\tCGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3051|1||HGNC|HGNC:4836,GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4411|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:8,7:2:9,0,18:..", + "chr16\t160089\tchr16_160089_TG_T\tTG\tT\t14\t.\tAF=0.5;AQ=14;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3032|1||HGNC|HGNC:4836,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4392|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:25,5:15:14,0,29:..", + "chr16\t160180\tchr16_160180_C_T\tC\tT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2942|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4302|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:29:1,28:15:15,25,0:..", + "chr16\t160216\tchr16_160216_T_A\tT\tA\t10\t.\tAF=1;AQ=10;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2906|1||HGNC|HGNC:4836,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4266|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,27:6:10,6,0:..", + "chr16\t160217\tchr16_160217_C_T\tC\tT\t9\t.\tAF=1;AQ=9;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2905|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4265|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:27:0,27:5:9,3,0:..", + "chr16\t160326\tchr16_160326_T_A\tT\tA\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2796|1||HGNC|HGNC:4836,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4156|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,29:14:15,18,0:..", + "chr16\t160327\tchr16_160327_C_T\tC\tT\t16\t.\tAF=1;AQ=16;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2795|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4155|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:29:3,26:14:16,17,0:..", + "chr16\t160388\tchr16_160388_G_GGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\tG\tGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\t15\t.\tAF=0.5;AQ=15;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2733|1||HGNC|HGNC:4836,GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4093|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:31:4,14:11:15,0,12:..", + "chr16\t160728\tchr16_160728_C_T\tC\tT\t5\t.\tAF=1;AQ=5;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2394|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3754|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:8,22:4:5,3,0:..", + "chr16\t160746\tchr16_160746_T_C\tT\tC\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2376|1||HGNC|HGNC:4836,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3736|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:23,7:10:10,0,18:..", + "chr16\t160751\tchr16_160751_AG_A;chr16_160752_G_GGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\tAG\tA\t8\t.\tAF=0.5;AQ=8;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2370|1||HGNC|HGNC:4836,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3730|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/0:22:.,7:6:0,0,0:..", + "chr16\t160752\tchr16_160751_AG_A;chr16_160752_G_GGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\tG\tGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\t8\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2369|1||HGNC|HGNC:4836,GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3729|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:.,14:6:0,0,0:..", + "chr16\t161210\tchr16_161210_GC_G\tGC\tG\t6\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1911|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4767|1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3271|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:27:21,5:7:6,0,27:..", + "chr16\t161474\tchr16_161474_TA_T\tTA\tT\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1647|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4503|1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3007|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:25:16,9:23:22,0,39:..", + "chr16\t162329\tchr16_162329_G_A\tG\tA\t23\t.\tAF=0.5;AQ=23;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||793|1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||3649|1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2153|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:24:23,0,41:..", + "chr16\t162650\tchr16_162650_C_T\tC\tT\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||472|1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||3328|1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1832|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:24:9,15:33:34,0,41:..", + "chr16\t163106\tchr16_163106_C_T\tC\tT\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||16|1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2872|1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1376|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:22:22,0,39:..", + "chr16\t163140\tchr16_163140_T_G\tT\tG\t17\t.\tAF=0.5;AQ=17;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|1/3||||19|||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2838|1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1342|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:17:17,0,39:..", + "chr16\t163143\tchr16_163143_G_A\tG\tA\t16\t.\tAF=0.5;AQ=16;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|1/3||||22|||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2835|1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1339|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:17:16,0,41:..", + "chr16\t163229\tchr16_163229_T_C\tT\tC\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2749|1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1253|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:3:0,0,27:..", + "chr16\t163796\tchr16_163796_T_A\tT\tA\t12\t.\tAF=1;AQ=12;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2182|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4883|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||686|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:15:0,15:7:12,7,0:..", + "chr16\t163800\tchr16_163800_G_A\tG\tA\t8\t.\tAF=1;AQ=8;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2178|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4879|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||682|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:16:2,14:3:8,0,0:..", + "chr16\t163804\tchr16_163804_G_A\tG\tA\t14\t.\tAF=1;AQ=14;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2174|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4875|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||678|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:13:14,16,0:..", + "chr16\t164431\tchr16_164431_T_TG\tT\tTG\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1546|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4247|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||50|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:22:25,25,0:..", + "chr16\t164541\tchr16_164541_G_GGTCC\tG\tGGTCC\t26\t.\tAF=0.5;AQ=26;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GTCC|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|2/3||||155-156|||||||1||HGNC|HGNC:4836,GTCC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1436|1||HGNC|HGNC:4826,GTCC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4137|1||HGNC|HGNC:4825,GTCC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GTCC|non_coding_transcript_exon_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|1/3||||60-61|||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:13,7:26:26,0,39:..", + "chr16\t164690\tchr16_164690_C_CGCGGGGCGCGGTGCGGGCGGG\tC\tCGCGGGGCGCGGTGCGGGCGGG\t27\t.\tAF=0.5;AQ=27;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGGGCGCGGTGCGGGCGGG|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGGGCGCGGTGCGGGCGGG|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1287|1||HGNC|HGNC:4826,GCGGGGCGCGGTGCGGGCGGG|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3988|1||HGNC|HGNC:4825,GCGGGGCGCGGTGCGGGCGGG|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGGGCGCGGTGCGGGCGGG|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:6,14:25:27,0,28:..", + "chr16\t164723\tchr16_164723_C_T\tC\tT\t11\t.\tAF=0.5;AQ=11;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1255|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3956|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:15,4:11:11,0,21:..", + "chr16\t164731\tchr16_164731_C_CG\tC\tCG\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1246|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3947|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:2,14:2:14,0,22:..", + "chr16\t164740\tchr16_164740_C_T\tC\tT\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1238|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3939|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:1,18:2:2,0,1:..", + "chr16\t164771\tchr16_164771_T_C\tT\tC\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1207|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3908|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:13,6:4:10,0,25:..", + "chr16\t164791\tchr16_164791_G_A\tG\tA\t16\t.\tAF=0.5;AQ=16;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1187|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3888|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:6,15:15:16,0,20:..", + "chr16\t164800\tchr16_164800_G_GGCGGGGTCGCGGGGCGGGGCGAGGTC\tG\tGGCGGGGTCGCGGGGCGGGGCGAGGTC\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGGGTCGCGGGGCGGGGCGAGGTC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1177|1||HGNC|HGNC:4826,GCGGGGTCGCGGGGCGGGGCGAGGTC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3878|1||HGNC|HGNC:4825,GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,4:5:4,0,19:..", + "chr16\t164817\tchr16_164817_C_A\tC\tA\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1161|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3862|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:8,13:21:22,0,27:..", + "chr16\t164831\tchr16_164831_C_CG\tC\tCG\t4\t.\tAF=1;AQ=4;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1146|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3847|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:4,15:2:4,0,0:..", + "chr16\t164839\tchr16_164839_G_GGT\tG\tGGT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GT|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1138|1||HGNC|HGNC:4826,GT|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3839|1||HGNC|HGNC:4825,GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:2,15:10:15,10,0:..", + "chr16\t164871\tchr16_164871_T_G\tT\tG\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1107|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3808|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:12,7:14:13,0,33:..", + "chr16\t164884\tchr16_164884_G_GT\tG\tGT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1093|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3794|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:15:15,22,0:..", + "chr16\t164892\tchr16_164892_CG_C\tCG\tC\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1085|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3786|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:18,3:5:2,0,21:..", + "chr16\t164907\tchr16_164907_C_A\tC\tA\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1071|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3772|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:12,8:5:3,0,20:..", + "chr16\t164931\tchr16_164931_C_G\tC\tG\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1047|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3748|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:1,8:5:3,0,19:..", + "chr16\t164932\tchr16_164932_G_GGGCGGGC\tG\tGGGCGGGC\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GGCGGGC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1045|1||HGNC|HGNC:4826,GGCGGGC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3746|1||HGNC|HGNC:4825,GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:2,7:4:1,0,15:..", + "chr16\t164942\tchr16_164942_G_GT\tG\tGT\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1035|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3736|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:0,8:6:4,0,14:..", + "chr16\t164953\tchr16_164953_G_GGCGGC\tG\tGGCGGC\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1024|1||HGNC|HGNC:4826,GCGGC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3725|1||HGNC|HGNC:4825,GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,6:13:13,0,33:..", + "chr16\t164985\tchr16_164985_C_CG\tC\tCG\t18\t.\tAF=1;AQ=18;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||992|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3693|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:19:1,18:16:18,18,0:..", + "chr16\t165212\tchr16_165212_TC_T\tTC\tT\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||57|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||765|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3466|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:18,3:5:3,0,30:..", + "chr16\t165380\tchr16_165380_G_A\tG\tA\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||224|1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||598|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3299|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,8:29:29,0,43:..", + "chr16\t165856\tchr16_165856_G_C\tG\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||700|1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||122|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2823|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,8:29:29,0,44:..", + "chr16\t166191\tchr16_166191_C_CG\tC\tCG\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1035|1||HGNC|HGNC:4836,G|intron_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2487|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,6:23:22,0,36:..", + "chr16\t166518\tchr16_166518_TG_T\tTG\tT\t11\t.\tAF=0.5;AQ=11;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1363|1||HGNC|HGNC:4836,-|intron_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding||2/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2160|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||2/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||2/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:16,4:12:11,0,32:..", + "chr16\t167928\tchr16_167928_GT_G\tGT\tG\t17\t.\tAF=0.5;AQ=17;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4947|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2773|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1165|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4961|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||750|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1168|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4965|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1168|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,6:17:17,0,31:..", + "chr16\t167947\tchr16_167947_T_TC\tT\tTC\t19\t.\tAF=0.5;AQ=19;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4928|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2791|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1183|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4942|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||731|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1186|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4946|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4996|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1186|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:11,10:18:19,0,22:..", + "chr16\t167948\tchr16_167948_T_C\tT\tC\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4928|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2792|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1184|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4942|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||731|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1187|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4946|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4996|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1187|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:10,10:10:10,0,17:..", + "chr16\t168533\tchr16_168533_T_C\tT\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4343|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3377|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1769|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4357|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||146|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1772|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4361|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4411|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1772|1||HGNC|HGNC:4826,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4969|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:29:29,0,43:..", + "chr16\t168736\tchr16_168736_A_G\tA\tG\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4140|1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3580|1||HGNC|HGNC:4836,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1972|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4154|1||HGNC|HGNC:4824,G|non_coding_transcript_exon_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|1/3||||58|||||||1||HGNC|HGNC:4825,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1975|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4158|1||HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4208|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1975|1||HGNC|HGNC:4826,G|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4766|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:34:34,0,48:..", + "chr16\t169117\tchr16_169117_TG_T\tTG\tT\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3758|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3962|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2354|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3772|1||HGNC|HGNC:4824,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2357|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3776|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3826|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2357|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4384|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:17,3:6:4,0,27:..", + "chr16\t169404\tchr16_169404_TC_T\tTC\tT\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3471|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||4249|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2641|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3485|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||71|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2644|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3489|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3539|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2644|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4097|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:16,2:7:5,0,30:..", + "chr16\t169624\tchr16_169624_TC_T\tTC\tT\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3251|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||4469|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2861|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3265|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||291|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2864|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3269|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3319|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2864|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3877|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,4:11:10,0,32:..", + "chr16\t170831\tchr16_170831_T_TCACA\tT\tTCACA\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||2044|1||HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4067|1||HGNC|HGNC:4826,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||2058|1||HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1497|1||HGNC|HGNC:4825,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||2062|1||HGNC|HGNC:4824,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2112|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2670|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:6,6:3:19,0,25:..", + "chr16\t170862\tchr16_170862_C_CACACA\tC\tCACACA\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||2013|1||HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4098|1||HGNC|HGNC:4826,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||2027|1||HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1528|1||HGNC|HGNC:4825,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4101|1||HGNC|HGNC:4826,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||2031|1||HGNC|HGNC:4824,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2081|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4101|1||HGNC|HGNC:4826,ACACA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2639|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,2:7:5,0,28:..", + "chr16\t170943\tchr16_170943_AG_A\tAG\tA\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1932|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4180|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1946|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1610|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4183|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1950|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2000|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4183|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2558|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:18,2:4:1,0,26:..", + "chr16\t171206\tchr16_171206_T_TTTA\tT\tTTTA\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4442|1||HGNC|HGNC:4826,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1683|1||HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1872|1||HGNC|HGNC:4825,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4445|1||HGNC|HGNC:4826,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1687|1||HGNC|HGNC:4824,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1737|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4445|1||HGNC|HGNC:4826,TTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2295|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:13:13,0,22:..", + "chr16\t171219\tchr16_171219_T_TTA\tT\tTTA\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1656|1||HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4455|1||HGNC|HGNC:4826,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1670|1||HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1885|1||HGNC|HGNC:4825,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4458|1||HGNC|HGNC:4826,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1674|1||HGNC|HGNC:4824,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1724|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4458|1||HGNC|HGNC:4826,TA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2282|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:14,3:4:1,0,20:..", + "chr16\t171220\tchr16_171220_T_TATTA\tT\tTATTA\t9\t.\tAF=0.5;AQ=9;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1655|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4456|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1886|1||HGNC|HGNC:4825,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1673|1||HGNC|HGNC:4824,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1723|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2281|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,4:10:9,0,23:..", + "chr16\t171534\tchr16_171534_AT_A\tAT\tA\t20\t.\tAF=0.5;AQ=20;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1341|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4771|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1355|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2201|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4774|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1359|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1409|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4774|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1967|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:14,5:20:20,0,40:..", + "chr16\t171881\tchr16_171881_TC_T\tTC\tT\t21\t.\tAF=0.5;AQ=21;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||994|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4798|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4822|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1008|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2548|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4816|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1012|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1062|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4866|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1620|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:21:21,0,35:.." + ], + [ + "chr16\t172418\tchr16_172418_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||458|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4262|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4286|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||472|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3084|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4280|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||476|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||526|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4330|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4895|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1084|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:16:20,17,0:..", + "chr16\t172636\tchr16_172636_C_T\tC\tT\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||240|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4044|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4068|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||254|1||HGNC|HGNC:4824,T|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3302|1||HGNC|HGNC:4825,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4062|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||258|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||308|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4112|1||HGNC|HGNC:4823,T|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4677|-1|||,T|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||866|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:1,17:14:23,14,0:..", + "chr16\t172870\tchr16_172870_G_C\tG\tC\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||6|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||3810|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||3834|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||20|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3536|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||3828|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||24|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||74|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3878|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4443|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||632|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:20:24,22,0:..", + "chr16\t173116\tchr16_173116_TC_T\tTC\tT\t6\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding||1/2||||||||||1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||3563|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||3587|1||HGNC|HGNC:4823,-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding||1/2||||||||||1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3783|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||3581|1||HGNC|HGNC:4823,-|non_coding_transcript_exon_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|1/2||||224|||||||1||HGNC|HGNC:4824,-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding||1/1||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3631|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4196|-1|||,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||385|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:16,3:8:6,0,30:..", + "chr16\t173707\tchr16_173707_A_G\tA\tG\t27\t.\tAF=1;AQ=27;AC=2;cadd_raw=0.19;cadd_phred=3.05;CSQ=G|3_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|3/3||||573|||||||1||HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||2973|1||HGNC|HGNC:4823,G|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||4847|1||RFAM|,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||2997|1||HGNC|HGNC:4823,G|3_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|3/3||||510|||||||1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4373|1||HGNC|HGNC:4825,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||2991|1||HGNC|HGNC:4823,G|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||32|1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||244|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3041|1||HGNC|HGNC:4823,G|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||3606|-1|||,G|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||47|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:19:0,19:25:27,27,0:..", + "chr16\t176848\tchr16_176848_GC_G\tGC\tG\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||3610|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3139|1||HGNC|HGNC:4824,-|intron_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding||1/2||||||||||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1705|1||RFAM|,-|intron_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding||1/2||||||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3139|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|1/2||||152|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3174|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3386|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron||1/1||||||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||464|-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3189|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:15,2:6:5,0,28:..", + "chr16\t176953\tchr16_176953_CA_C\tCA\tC\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||3505|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3244|1||HGNC|HGNC:4824,-|frameshift_variant|HIGH|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|2/3||||158|121|41|K/X|Aag/ag|||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1600|1||RFAM|,-|frameshift_variant|HIGH|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|2/3||||85|25|9|K/X|Aag/ag|||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3244|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|1/2||||257|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3279|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3491|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|2/2||||90|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||359|-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3294|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:15,2:7:5,0,30:..", + "chr16\t177485\tchr16_177485_AC_A\tAC\tA\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||2973|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3776|1||HGNC|HGNC:4824,-|3_prime_UTR_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|3/3||||541|||||||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1068|1||RFAM|,-|3_prime_UTR_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|3/3||||468|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3776|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|2/2||||640|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3811|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4023|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||212|1||HGNC|HGNC:4823,-|non_coding_transcript_exon_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|1/1||||5|||||||-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3826|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:13,4:6:5,0,31:..", + "chr16\t274052\tchr16_274052_A_G\tA\tG\t28\t.\tAF=1;AQ=28;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|synonymous_variant&NMD_transcript_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000168869|nonsense_mediated_decay|5/15||||353|250|84|L|Tta/Cta|||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000301679|protein_coding|||||||||||3972|1||HGNC|HGNC:14163,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000316163|protein_coding|6/17||||434|357|119|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000359740|protein_coding|5/16||||387|387|129|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000397770|protein_coding|6/17||||453|420|140|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000472466|retained_intron|||||||||||887|-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000477143|retained_intron|1/9||||905|||||||-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000481672|retained_intron|2/11||||110|||||||-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000493449|retained_intron|5/9||||1199|||||||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000600536|nonsense_mediated_decay|||||||||||4109|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000653392|nonsense_mediated_decay|||||||||||4216|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000654053|nonsense_mediated_decay|||||||||||4154|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000659283|nonsense_mediated_decay|||||||||||1869|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000666018|nonsense_mediated_decay|||||||||||4097|1||HGNC|HGNC:14163\tGT:DP:AD:GQ:PL:RNC\t1/1:32:0,32:26:28,29,0:..", + "chr16\t286660\tchr16_286660_G_A\tG\tA\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000219406|protein_coding|9/11||||1353|1347|449|T|acG/acA|||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000219409|protein_coding|||||||||||3650|1||HGNC|HGNC:680,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding|||||||||||780|-1||HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding|||||||||||781|-1||HGNC|HGNC:903,A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000404312|protein_coding|9/11||||1343|1338|446|T|acG/acA|||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000414650|protein_coding|||||||||||3850|1|cds_end_NF|HGNC|HGNC:680,A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000435833|protein_coding|3/5||||234|234|78|T|acG/acA|||1|cds_start_NF|HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000447871|protein_coding|||||||||||3972|1|cds_end_NF|HGNC|HGNC:680,A|downstream_gene_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000456379|protein_coding|||||||||||1520|1|cds_start_NF&cds_end_NF|HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000457798|protein_coding|||||||||||1530|-1|cds_start_NF|HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron|||||||||||780|-1||HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000462950|protein_coding_CDS_not_defined|||||||||||1084|1||HGNC|HGNC:14180,A|non_coding_transcript_exon_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000467212|retained_intron|8/10||||1418|||||||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000477621|retained_intron|||||||||||3820|1||HGNC|HGNC:680,A|non_coding_transcript_exon_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000482665|retained_intron|5/7||||1630|||||||1||HGNC|HGNC:14180\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:19:25,19,0:..", + "chr16\t309953\tchr16_309953_A_G\tA\tG\t33\t.\tAF=0.5;AQ=33;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding||4/10||||||||||-1||HGNC|HGNC:903,G|intron_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding||4/9||||||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron||3/7||||||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000481769|protein_coding_CDS_not_defined||3/4||||||||||-1||HGNC|HGNC:903\tGT:DP:AD:GQ:PL:RNC\t0/1:11:6,5:33:33,0,44:..", + "chr16\t346264\tchr16_346264_A_G\tA\tG\t31\t.\tAF=0.5;AQ=31;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|synonymous_variant|LOW|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding|2/11||||1198|762|254|D|gaT/gaC|||-1||HGNC|HGNC:903,G|synonymous_variant|LOW|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding|2/10||||924|762|254|D|gaT/gaC|||-1||HGNC|HGNC:903,G|non_coding_transcript_exon_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron|1/8||||59|||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000481769|protein_coding_CDS_not_defined||1/4||||||||||-1||HGNC|HGNC:903\tGT:DP:AD:GQ:PL:RNC\t0/1:26:15,11:31:31,0,40:..", + "chr16\t377013\tchr16_377013_G_C\tG\tC\t28\t.\tAF=0.5;AQ=28;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000250930|protein_coding||4/12||||||||||-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000424078|protein_coding|||||||||||2162|-1|cds_start_NF|HGNC|HGNC:17205,C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000427313|protein_coding||4/4||||||||||-1|cds_end_NF|HGNC|HGNC:17205,C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000431232|protein_coding||4/12||||||||||-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000448854|protein_coding|||||||||||1798|-1|cds_start_NF|HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000467452|retained_intron|||||||||||1938|-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000475348|retained_intron|||||||||||538|-1||HGNC|HGNC:17205,C|downstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000476735|protein_coding_CDS_not_defined|||||||||||95|-1||HGNC|HGNC:17205\tGT:DP:AD:GQ:PL:RNC\t0/1:17:11,6:29:28,0,42:..", + "chr16\t520623\tchr16_520623_G_A\tG\tA\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000262305|protein_coding||13/13||||||||||1||HGNC|HGNC:17224,A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000434585|protein_coding||14/14||||||||||1||HGNC|HGNC:17224,A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000450428|protein_coding||11/11||||||||||1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000461009|retained_intron|||||||||||1515|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000464263|retained_intron|||||||||||861|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000487899|retained_intron|||||||||||1605|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|LINC00235|ENSG00000277142|Transcript|ENST00000622160|lncRNA|||||||||||4532|-1||HGNC|HGNC:14138\tGT:DP:AD:GQ:PL:RNC\t0/1:18:9,9:34:34,0,44:..", + "chr16\t551632\tchr16_551632_T_C\tT\tC\t21\t.\tAF=1;AQ=21;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|synonymous_variant|LOW|CAPN15|ENSG00000103326|Transcript|ENST00000219611|protein_coding|9/14||||2820|2313|771|G|ggT/ggC|||1||HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000562370|protein_coding|||||||||||4240|1|cds_end_NF|HGNC|HGNC:11182,C|upstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000565010|retained_intron|||||||||||665|1||HGNC|HGNC:11182,C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000261691|Transcript|ENST00000565879|lncRNA||1/1||||||||||-1|||,C|upstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000566977|protein_coding|||||||||||1123|1|cds_start_NF|HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000568988|protein_coding|||||||||||3423|1|cds_end_NF|HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000637507|protein_coding|||||||||||3601|1|cds_end_NF|HGNC|HGNC:11182\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:15:21,16,0:..", + "chr16\t582180\tchr16_582180_G_C\tG\tC\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000026218|protein_coding||9/9||||||||||1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000321878|protein_coding||9/10||||||||||1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000409527|protein_coding||10/11||||||||||1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000420990|nonsense_mediated_decay||6/7||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000422307|protein_coding|||||||||||4946|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000443147|nonsense_mediated_decay||10/11||||||||||1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000470411|protein_coding|||||||||||4963|1||HGNC|HGNC:14135,C|non_coding_transcript_exon_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000476438|retained_intron|1/2||||420|||||||1||HGNC|HGNC:14135,C|intron_variant&non_coding_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000480424|retained_intron||3/4||||||||||1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000537901|retained_intron|||||||||||3378|1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000540241|protein_coding||2/3||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000540548|protein_coding_CDS_not_defined|||||||||||310|1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000544860|protein_coding_CDS_not_defined|||||||||||3337|1||HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000634341|retained_intron|||||||||||697|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635205|nonsense_mediated_decay||3/4||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635909|nonsense_mediated_decay||8/9||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635935|protein_coding_CDS_not_defined|||||||||||1403|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000636005|nonsense_mediated_decay||8/9||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000636657|nonsense_mediated_decay||10/11||||||||||1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000637468|nonsense_mediated_decay||6/7||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000638143|nonsense_mediated_decay|||||||||||1258|1|cds_start_NF|HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000638152|protein_coding_CDS_not_defined|||||||||||1404|1||HGNC|HGNC:14135\tGT:DP:AD:GQ:PL:RNC\t1/1:6:0,6:9:25,8,0:..", + "chr16\t627629\tchr16_627629_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000248139|protein_coding|6/6||||1079|||||||1||HGNC|HGNC:18285,C|upstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000319070|protein_coding|||||||||||3356|1||HGNC|HGNC:30912,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000509637|nonsense_mediated_decay|||||||||||1636|1|cds_start_NF|HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000535977|protein_coding|7/7||||1075|||||||1||HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000538492|protein_coding|7/7||||927|||||||1||HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000539661|protein_coding|7/7||||967|||||||1||HGNC|HGNC:18285,C|non_coding_transcript_exon_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000561781|retained_intron|2/2||||796|||||||1||HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000563109|protein_coding|||||||||||46|1|cds_start_NF&cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000564703|protein_coding|||||||||||1512|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000565511|nonsense_mediated_decay|||||||||||1546|1||HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000566290|protein_coding|||||||||||214|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000568586|protein_coding|||||||||||1508|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000569575|protein_coding|||||||||||1603|1|cds_end_NF|HGNC|HGNC:18285,C|upstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000573440|retained_intron|||||||||||1610|1||HGNC|HGNC:30912\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:13:20,13,0:..", + "chr16\t638557\tchr16_638557_A_C\tA\tC\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000301686|protein_coding|||||||||||2252|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000307650|protein_coding|||||||||||3271|1||HGNC|HGNC:14142,C|downstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000319070|protein_coding|||||||||||4440|1||HGNC|HGNC:30912,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000338401|protein_coding|||||||||||2215|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397664|protein_coding|||||||||||2206|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397665|protein_coding|||||||||||2267|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397666|protein_coding|||||||||||2255|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000448973|retained_intron|||||||||||2247|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000456420|nonsense_mediated_decay|||||||||||2318|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000474840|nonsense_mediated_decay|||||||||||3372|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000491999|nonsense_mediated_decay|||||||||||3289|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000564039|nonsense_mediated_decay|||||||||||2279|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000565163|protein_coding|||||||||||2297|-1|cds_start_NF&cds_end_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000565799|retained_intron|||||||||||2290|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568077|nonsense_mediated_decay|||||||||||2226|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568773|protein_coding|||||||||||2322|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568830|protein_coding|||||||||||2199|-1|cds_end_NF|HGNC|HGNC:14141,C|downstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000573440|retained_intron|||||||||||4441|1||HGNC|HGNC:30912,C|intron_variant&non_coding_transcript_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000611328|protein_coding_CDS_not_defined||1/3||||||||||1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000614890|protein_coding|||||||||||2191|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000615744|protein_coding_CDS_not_defined|||||||||||3894|1||HGNC|HGNC:14142,C|non_coding_transcript_exon_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000619114|protein_coding_CDS_not_defined|2/2||||576|||||||1||HGNC|HGNC:14142,C|non_coding_transcript_exon_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000619377|protein_coding_CDS_not_defined|2/2||||664|||||||1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000620462|retained_intron|||||||||||3926|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000629534|protein_coding|||||||||||3292|1||HGNC|HGNC:14142\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:16:24,17,0:..", + "chr16\t655844\tchr16_655844_T_C\tT\tC\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000293879|protein_coding|17/41||||1973|1921|641|L|Ttg/Ctg|||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000420061|retained_intron|17/17||||1985|||||||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546516|retained_intron|3/20||||614|||||||1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547407|retained_intron|||||||||||431|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548844|protein_coding_CDS_not_defined|||||||||||2716|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548859|retained_intron|||||||||||589|1||HGNC|HGNC:26960,C|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000549091|protein_coding|17/41||||2013|1921|641|L|Ttg/Ctg|||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000549648|retained_intron|17/17||||1988|||||||1||HGNC|HGNC:26960,C|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000550593|retained_intron|||||||||||2374|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000550739|protein_coding|||||||||||3401|1|cds_start_NF&cds_end_NF|HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552648|protein_coding_CDS_not_defined|4/7||||455|||||||1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552683|retained_intron|||||||||||2014|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552728|nonsense_mediated_decay|||||||||||577|1|cds_start_NF|HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552943|retained_intron|15/26||||3591|||||||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER||ENSG00000262528|Transcript|ENST00000573609|lncRNA|1/2||||351|||||||-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:16:23,17,0:..", + "chr16\t667523\tchr16_667523_G_T\tG\tT\t27\t.\tAF=1;AQ=27;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000293879|protein_coding|41/41||||5233|5181|1727|P|ccG/ccT|||1||HGNC|HGNC:26960,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000315082|protein_coding|||||||||||609|1||HGNC|HGNC:21169,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000315764|protein_coding|6/6||||1147|834|278|P|ccG/ccT|||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546516|retained_intron|||||||||||4090|1||HGNC|HGNC:26960,T|missense_variant|MODERATE|WDR90|ENSG00000161996|Transcript|ENST00000546896|protein_coding|2/2||||89|89|30|R/L|cGt/cTt|||1|cds_start_NF|HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546923|retained_intron|||||||||||4787|1||HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547407|retained_intron|24/24||||3541|||||||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547543|protein_coding_CDS_not_defined|||||||||||778|1||HGNC|HGNC:26960,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000547944|protein_coding|7/7||||1365|978|326|P|ccG/ccT|||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548448|retained_intron|||||||||||1162|1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548603|protein_coding_CDS_not_defined|||||||||||4086|1||HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000549024|retained_intron|12/12||||1951|||||||1||HGNC|HGNC:26960,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000549091|protein_coding|41/41||||5279|5187|1729|P|ccG/ccT|||1||HGNC|HGNC:26960,T|3_prime_UTR_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000551100|protein_coding|3/3||||315|||||||1|cds_start_NF|HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552683|retained_intron|||||||||||4085|1||HGNC|HGNC:26960,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552728|nonsense_mediated_decay|22/22||||2826|||||||1|cds_start_NF|HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000553080|retained_intron|6/6||||1635|||||||1||HGNC|HGNC:26960,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561711|retained_intron|||||||||||4394|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561929|protein_coding|||||||||||686|1|cds_start_NF&cds_end_NF|HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561983|nonsense_mediated_decay|||||||||||582|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562333|nonsense_mediated_decay|||||||||||664|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562598|retained_intron|||||||||||659|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562708|retained_intron|||||||||||589|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563134|protein_coding|||||||||||583|1|cds_end_NF|HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563637|nonsense_mediated_decay|||||||||||628|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563776|retained_intron|||||||||||582|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000565004|retained_intron|||||||||||3559|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000566214|nonsense_mediated_decay|||||||||||628|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000566965|retained_intron|||||||||||1037|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000567017|retained_intron|||||||||||639|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000567589|retained_intron|||||||||||3005|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000568636|retained_intron|||||||||||1135|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000568950|retained_intron|||||||||||655|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569358|retained_intron|||||||||||2932|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569675|retained_intron|||||||||||612|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569706|retained_intron|||||||||||609|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569943|protein_coding_CDS_not_defined|||||||||||830|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000570092|retained_intron|||||||||||601|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000570280|nonsense_mediated_decay|||||||||||630|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000602564|retained_intron|||||||||||657|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000697194|protein_coding|||||||||||577|1||HGNC|HGNC:21169\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:23:27,24,0:..", + "chr16\t690466\tchr16_690466_A_G\tA\tG\t26\t.\tAF=1;AQ=26;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000248142|protein_coding|||||||||||22|-1||HGNC|HGNC:20852,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000293883|protein_coding|||||||||||68|-1||HGNC|HGNC:20852,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000397621|protein_coding|||||||||||2034|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562563|protein_coding|||||||||||2461|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562585|protein_coding_CDS_not_defined|||||||||||4192|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562648|retained_intron|||||||||||2032|-1||HGNC|HGNC:14150,G|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000261659|Transcript|ENST00000566927|lncRNA||1/1||||||||||1|||,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000567014|retained_intron|||||||||||3537|-1||HGNC|HGNC:20852,G|non_coding_transcript_exon_variant|MODIFIER||ENSG00000261659|Transcript|ENST00000575305|retained_intron|1/1||||1466|||||||1|||,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000647644|protein_coding|||||||||||219|-1||HGNC|HGNC:20852\tGT:DP:AD:GQ:PL:RNC\t1/1:17:0,17:20:26,21,0:..", + "chr16\t723341\tchr16_723341_G_A\tG\tA\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000219535|protein_coding|||||||||||768|1||HGNC|HGNC:14152,A|intron_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000293889|protein_coding||11/13||||||||||-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000341413|protein_coding|||||||||||3617|1||HGNC|HGNC:14177,A|intron_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000345165|protein_coding||11/13||||||||||-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000389701|retained_intron|||||||||||4064|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000389703|protein_coding|||||||||||3765|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000423653|protein_coding_CDS_not_defined|||||||||||1586|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000439619|retained_intron|||||||||||1209|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000460023|retained_intron|||||||||||1566|-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000463539|retained_intron||9/11||||||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000466708|retained_intron||10/12||||||||||-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000471861|retained_intron|||||||||||1660|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000474647|retained_intron|||||||||||1782|-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000478979|retained_intron|4/4||||2296|||||||-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000481804|retained_intron|4/5||||2627|||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000482152|retained_intron||3/4||||||||||-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000482878|retained_intron|4/4||||2699|||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000485091|retained_intron||10/11||||||||||-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000538176|retained_intron|||||||||||1201|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000544996|retained_intron|||||||||||1643|-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000549114|protein_coding|||||||||||3595|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000561546|protein_coding|||||||||||3905|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000561750|retained_intron|||||||||||3934|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000562141|protein_coding|||||||||||3778|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000562187|protein_coding|||||||||||3765|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000563792|protein_coding|||||||||||4398|1|cds_end_NF|HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000564000|protein_coding|||||||||||756|1||HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000564537|protein_coding|||||||||||3765|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000564545|protein_coding|||||||||||3921|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000564640|retained_intron|||||||||||1029|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000566437|retained_intron|||||||||||833|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000566525|retained_intron|||||||||||752|1||HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000567414|protein_coding|||||||||||3952|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000567696|retained_intron|||||||||||3977|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000568141|protein_coding|||||||||||4005|1|cds_end_NF|HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|METRN|ENSG00000103260|Transcript|ENST00000568223|protein_coding|||||||||||3686|1||HGNC|HGNC:14151,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000568916|protein_coding|||||||||||751|1|cds_start_NF|HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000569143|retained_intron|||||||||||3977|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000569529|protein_coding|||||||||||751|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000570237|retained_intron|||||||||||751|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000650995|protein_coding|||||||||||2453|-1|cds_end_NF|HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000682391|retained_intron||7/9||||||||||-1||HGNC|HGNC:14153\tGT:DP:AD:GQ:PL:RNC\t1/1:17:0,17:19:23,21,0:..", + "chr16\t739761\tchr16_739761_A_G\tA\tG\t22\t.\tAF=1;AQ=22;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000251588|protein_coding||1/10||||||||||-1||HGNC|HGNC:14179,G|5_prime_UTR_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000540986|protein_coding|1/10||||1174|||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000562421|protein_coding|||||||||||2006|-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000562752|retained_intron||1/4||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000563534|protein_coding_CDS_not_defined|||||||||||2297|-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565065|nonsense_mediated_decay||2/5||||||||||-1||HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565341|retained_intron||1/3||||||||||-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565425|nonsense_mediated_decay||1/9||||||||||-1||HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565693|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14179,G|intron_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000566614|protein_coding||1/4||||||||||-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567172|protein_coding_CDS_not_defined||1/1||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567403|protein_coding|||||||||||2009|-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567455|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000568545|protein_coding|||||||||||1872|-1||HGNC|HGNC:14179,G|downstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000569604|protein_coding_CDS_not_defined|||||||||||4236|1||HGNC|HGNC:14177,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000569759|protein_coding_CDS_not_defined|||||||||||3391|-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000570066|nonsense_mediated_decay||1/4||||||||||-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000570289|nonsense_mediated_decay||1/3||||||||||-1||HGNC|HGNC:14179,G|downstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000647875|protein_coding_CDS_not_defined|||||||||||4408|1||HGNC|HGNC:14177\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:14:22,14,0:..", + "chr16\t766294\tchr16_766294_T_G\tT\tG\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000382862|protein_coding||11/16||||||||||1||HGNC|HGNC:7371,G|upstream_gene_variant|MODIFIER|MIR662|ENSG00000207579|Transcript|ENST00000384847|miRNA|||||||||||3889|1||HGNC|HGNC:32918,G|downstream_gene_variant|MODIFIER|MSLNL|ENSG00000162006|Transcript|ENST00000543963|protein_coding|||||||||||3134|-1|cds_start_NF|HGNC|HGNC:14170,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000545450|protein_coding||12/17||||||||||1||HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000561896|protein_coding||2/6||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000563651|protein_coding||10/10||||||||||1|cds_end_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000563941|protein_coding||12/17||||||||||1||HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000566269|protein_coding||2/7||||||||||1|cds_start_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000566549|protein_coding||11/16||||||||||1||HGNC|HGNC:7371,G|downstream_gene_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000569566|protein_coding|||||||||||1258|1|cds_end_NF|HGNC|HGNC:7371,G|downstream_gene_variant|MODIFIER||ENSG00000279136|Transcript|ENST00000623562|TEC|||||||||||2825|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:29:29,0,43:..", + "chr16\t789996\tchr16_789996_T_C\tT\tC\t36\t.\tAF=0.5;AQ=36;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000007264|protein_coding|||||||||||1615|-1||HGNC|HGNC:14173,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000262315|protein_coding||4/21||||||||||1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000317063|protein_coding||4/21||||||||||1||HGNC|HGNC:18435,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|CHTF18|ENSG00000127586|Transcript|ENST00000426047|protein_coding||2/6||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:18435,C|intron_variant&NMD_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000440239|nonsense_mediated_decay||4/13||||||||||1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000455171|protein_coding||3/20||||||||||1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000461268|protein_coding_CDS_not_defined|||||||||||2528|1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000464728|retained_intron||3/17||||||||||1||HGNC|HGNC:18435,C|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|CHTF18|ENSG00000127586|Transcript|ENST00000471202|retained_intron||4/18||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000479976|retained_intron||4/6||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000484349|retained_intron||1/3||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000491530|protein_coding_CDS_not_defined||2/5||||||||||1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000493715|protein_coding_CDS_not_defined|||||||||||4706|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000561734|protein_coding|||||||||||2015|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000562070|protein_coding|||||||||||2527|-1|cds_start_NF|HGNC|HGNC:14173,C|downstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000563545|nonsense_mediated_decay|||||||||||360|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000563560|protein_coding|||||||||||1667|-1|cds_end_NF|HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565377|protein_coding|||||||||||1615|-1|cds_end_NF|HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565503|nonsense_mediated_decay|||||||||||1656|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000565787|retained_intron|||||||||||1141|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565809|protein_coding|||||||||||1625|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000567114|protein_coding|||||||||||1599|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000567283|nonsense_mediated_decay|||||||||||1663|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000567620|retained_intron|||||||||||703|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000569270|nonsense_mediated_decay|||||||||||255|1|cds_start_NF|HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000569601|protein_coding|||||||||||1662|-1|cds_end_NF|HGNC|HGNC:14173,C|downstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000570058|protein_coding_CDS_not_defined|||||||||||656|1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000631357|protein_coding||5/23||||||||||1||HGNC|HGNC:18435\tGT:DP:AD:GQ:PL:RNC\t0/1:15:7,8:36:36,0,49:..", + "chr16\t813336\tchr16_813336_T_C\tT\tC\t32\t.\tAF=0.5;AQ=32;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER||ENSG00000287855|Transcript|ENST00000655150|lncRNA|||||||||||4153|1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:14:5,9:32:32,0,39:..", + "chr16\t893361\tchr16_893361_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||4/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||5/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||6/7||||||||||-1||HGNC|HGNC:14154,C|upstream_gene_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000565198|retained_intron|||||||||||109|-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding||3/5||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||3/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||4/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||4/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,45:..", + "chr16\t947473\tchr16_947473_T_C\tT\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||2/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||2/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||2/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding||2/3||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|5_prime_UTR_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding|1/6||||172|||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||2/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||2/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||2/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||2/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:23:8,15:30:29,0,47:..", + "chr16\t964119\tchr16_964119_A_G\tA\tG\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||1/10||||||||||-1||HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||1/7||||||||||-1||HGNC|HGNC:14154,G|missense_variant|MODERATE|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding|1/4||||4|4|2|Y/H|Tat/Cat|||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant&non_coding_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566609|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||1/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||1/9||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||1/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,G|downstream_gene_variant|MODIFIER||ENSG00000276931|Transcript|ENST00000620075|lncRNA|||||||||||4256|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:29:0,29:21:24,24,0:..", + "chr16\t977069\tchr16_977069_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|SOX8|ENSG00000005513|Transcript|ENST00000293894|protein_coding|||||||||||4701|1||HGNC|HGNC:11203,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000562570|lncRNA|2/2||||1914|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563837|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563863|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565069|lncRNA|3/3||||265|||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565139|lncRNA|||||||||||143|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565467|lncRNA||1/1||||||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000567961|lncRNA|||||||||||157|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000568394|lncRNA||1/2||||||||||-1||HGNC|HGNC:53928,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000655952|lncRNA|3/3||||743|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000662104|lncRNA|3/3||||322|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000669274|lncRNA|3/3||||225|||||||-1||HGNC|HGNC:53928\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,44:.." + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-08-12T10:10:59.241809478" + } +} \ No newline at end of file diff --git a/subworkflows/local/annotate_svs/tests/nextflow.config b/subworkflows/local/annotate_svs/tests/nextflow.config new file mode 100644 index 00000000..aceda89d --- /dev/null +++ b/subworkflows/local/annotate_svs/tests/nextflow.config @@ -0,0 +1,14 @@ +process { + + withName: 'UNTAR' { + ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' } + } + + withName: 'ENSEMBLVEP_SV' { + ext.args = { [ + '--offline', + '--vcf', + '--compress_output bgzip' + ].join(' ') } + } +} diff --git a/subworkflows/local/snv_annotation/main.nf b/subworkflows/local/snv_annotation/main.nf index 1bcc22e7..82fd3695 100644 --- a/subworkflows/local/snv_annotation/main.nf +++ b/subworkflows/local/snv_annotation/main.nf @@ -1,8 +1,8 @@ include { ANNOTATE_CADD } from '../annotate_cadd/main' include { ECHTVAR_ANNO } from '../../../modules/local/echtvar/anno/main' include { BCFTOOLS_FILLTAGS as BCFTOOLS_FILLTAGS_ANNO } from '../../../modules/local/bcftools/filltags/main' -include { ENSEMBLVEP_VEP } from '../../../modules/nf-core/ensemblvep/vep/main' -include { TABIX_TABIX as TABIX_VEP } from '../../../modules/nf-core/tabix/tabix/main' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_SNV } from '../../../modules/nf-core/ensemblvep/vep/main' +include { TABIX_TABIX as TABIX_ENSEMBLVEP_SNV } from '../../../modules/nf-core/tabix/tabix/main' workflow SNV_ANNOTATION { @@ -53,7 +53,7 @@ workflow SNV_ANNOTATION { } - ENSEMBLVEP_VEP ( + ENSEMBLVEP_SNV ( ch_vep_in, "GRCh38", "homo_sapiens", @@ -62,13 +62,13 @@ workflow SNV_ANNOTATION { ch_fasta, ch_vep_extra_files ) - ch_versions = ch_versions.mix(ENSEMBLVEP_VEP.out.versions) + ch_versions = ch_versions.mix(ENSEMBLVEP_SNV.out.versions) - TABIX_VEP ( ENSEMBLVEP_VEP.out.vcf ) - ch_versions = ch_versions.mix(TABIX_VEP.out.versions) + TABIX_ENSEMBLVEP_SNV ( ENSEMBLVEP_SNV.out.vcf ) + ch_versions = ch_versions.mix(TABIX_ENSEMBLVEP_SNV.out.versions) emit: - vcf = ENSEMBLVEP_VEP.out.vcf - tbi = TABIX_VEP.out.tbi + vcf = ENSEMBLVEP_SNV.out.vcf + tbi = TABIX_ENSEMBLVEP_SNV.out.tbi versions = ch_versions } diff --git a/subworkflows/local/snv_annotation/tests/nextflow.config b/subworkflows/local/snv_annotation/tests/nextflow.config index 791380d6..746f9c59 100644 --- a/subworkflows/local/snv_annotation/tests/nextflow.config +++ b/subworkflows/local/snv_annotation/tests/nextflow.config @@ -65,7 +65,7 @@ process { ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' } } - withName: 'SNV_ANNOTATION:ENSEMBLVEP_VEP' { + withName: 'SNV_ANNOTATION:ENSEMBLVEP_SNV' { ext.args = { [ '--offline', '--vcf', diff --git a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf index 5c4bb187..0291099f 100644 --- a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf @@ -36,6 +36,7 @@ def workflowSkips = [ mapping : "skip_mapping_wf", snv_calling : "skip_short_variant_calling", snv_annotation : "skip_snv_annotation", + sv_annotation : "skip_sv_annotation", call_paralogs : "skip_call_paralogs", cnv_calling : "skip_cnv_calling", phasing : "skip_phasing_wf", @@ -54,6 +55,7 @@ def workflowDependencies = [ call_paralogs : ["mapping"], snv_calling : ["mapping"], qc : ["mapping"], + sv_annotation : ["mapping"], snv_annotation : ["mapping", "snv_calling"], cnv_calling : ["mapping", "snv_calling"], phasing : ["mapping", "snv_calling"], @@ -71,6 +73,7 @@ def fileDependencies = [ assembly : ["fasta", "par_regions"], // The assembly workflow should be split into two - assembly and variant calling (requires ref) snv_calling : ["fasta", "par_regions"], snv_annotation : ["snp_db", "vep_cache", "vep_plugin_files", "variant_consequences_snv"], + sv_annotation : ["svdb_dbs", "vep_cache", "vep_plugin_files"], cnv_calling : ["hificnv_xy", "hificnv_xx", "hificnv_exclude"], rank_variants : ["reduced_penetrance", "score_config_snv"], repeat_calling : ["trgt_repeats"], @@ -86,6 +89,7 @@ def parameterStatus = [ skip_repeat_calling : params.skip_repeat_calling, skip_repeat_annotation : params.skip_repeat_annotation, skip_snv_annotation : params.skip_snv_annotation, + skip_sv_annotation : params.skip_sv_annotation, skip_call_paralogs : params.skip_call_paralogs, skip_cnv_calling : params.skip_cnv_calling, skip_mapping_wf : params.skip_mapping_wf, @@ -95,6 +99,7 @@ def parameterStatus = [ files: [ par_regions : params.par_regions, snp_db : params.snp_db, + svdb_dbs : params.svdb_dbs, somalier_sites : params.somalier_sites, vep_cache : params.vep_cache, hificnv_xy : params.hificnv_xy, diff --git a/tests/main.nf.test b/tests/main.nf.test index 9f5fc3e5..de6147be 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -11,7 +11,7 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/' input = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv' outdir = "$outputDir" } @@ -78,8 +78,8 @@ nextflow_pipeline { { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz.tbi").exists() }, { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz").exists() }, { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/svs/multi_sample/test/test_svs.vcf.gz").exists() }, - { assert new File("$outputDir/svs/multi_sample/test/test_svs.vcf.gz.tbi").exists() }, + { assert new File("$outputDir/svs/multi_sample/test/test_svs_annotated.vcf.gz").exists() }, + { assert new File("$outputDir/svs/multi_sample/test/test_svs_annotated.vcf.gz.tbi").exists() }, // Assert exists HG002_Revio { assert new File("$outputDir/aligned_reads/HG002_Revio/HG002_Revio_haplotagged.bam.bai").exists() }, { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio/HG002_Revio.hap1.bam.bai").exists() }, @@ -121,7 +121,7 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/' input = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam.csv' outdir = "$outputDir" parallel_snv = 2 @@ -226,8 +226,8 @@ nextflow_pipeline { { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() }, { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz").exists() }, { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/svs/multi_sample/test/test_svs.vcf.gz").exists() }, - { assert new File("$outputDir/svs/multi_sample/test/test_svs.vcf.gz.tbi").exists() }, + { assert new File("$outputDir/svs/multi_sample/test/test_svs_annotated.vcf.gz").exists() }, + { assert new File("$outputDir/svs/multi_sample/test/test_svs_annotated.vcf.gz.tbi").exists() }, { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz").exists() }, { assert new File("$outputDir/repeat_calling/trgt/multi_sample/test/test.vcf.gz.tbi").exists() }, // Assert exists HG002_Revio_A @@ -305,7 +305,7 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/' input = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam_ont.csv' outdir = "$outputDir" preset = 'ONT_R10' @@ -374,8 +374,8 @@ nextflow_pipeline { { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() }, { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz").exists() }, { assert new File("$outputDir/snvs/multi_sample/test/test_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/svs/multi_sample/test/test_svs.vcf.gz").exists() }, - { assert new File("$outputDir/svs/multi_sample/test/test_svs.vcf.gz.tbi").exists() }, + { assert new File("$outputDir/svs/multi_sample/test/test_svs_annotated.vcf.gz").exists() }, + { assert new File("$outputDir/svs/multi_sample/test/test_svs_annotated.vcf.gz.tbi").exists() }, // Assert exists HG002_ONT_A { assert new File("$outputDir/aligned_reads/HG002_ONT_A/HG002_ONT_A_haplotagged.bam.bai").exists() }, { assert new File("$outputDir/cnv_calling/hificnv/HG002_ONT_A/HG002_ONT_A.log").exists() }, diff --git a/workflows/nallo.nf b/workflows/nallo.nf index 60a703a6..79c47956 100644 --- a/workflows/nallo.nf +++ b/workflows/nallo.nf @@ -7,6 +7,7 @@ include { samplesheetToList } from 'plugin/nf-schema' */ include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SNV } from '../subworkflows/local/annotate_consequence_pli' +include { ANNOTATE_SVS } from '../subworkflows/local/annotate_svs' include { ANNOTATE_REPEAT_EXPANSIONS } from '../subworkflows/local/annotate_repeat_expansions' include { ASSEMBLY } from '../subworkflows/local/genome_assembly' include { ASSEMBLY_VARIANT_CALLING } from '../subworkflows/local/assembly_variant_calling' @@ -104,6 +105,8 @@ workflow NALLO { : Channel.value([]) ch_somalier_sites = params.somalier_sites ? Channel.fromPath(params.somalier_sites).map { [ it.simpleName, it ] }.collect() : '' + ch_svdb_dbs = params.svdb_dbs ? Channel.fromPath(params.svdb_dbs).map { [ it.simpleName, it ] }.collect() + : '' // Check parameter that doesn't conform to schema validation here if (params.phaser.matches('hiphase') && params.preset == 'ONT_R10') { error "The HiPhase license only permits analysis of data from PacBio. For details see: https://github.com/PacificBiosciences/HiPhase/blob/main/LICENSE.md" } @@ -310,6 +313,21 @@ workflow NALLO { ) ch_versions = ch_versions.mix(CALL_SVS.out.versions) + + // + // Annotate structural variants + // + if(!params.skip_sv_annotation) { + ANNOTATE_SVS ( + CALL_SVS.out.ch_multisample_vcf, + fasta, + ch_svdb_dbs, + ch_vep_cache, + params.vep_cache_version, + ch_vep_extra_files + ) + } + // // Call (and annotate and rank) SNVs // From 18ab1c0e75cb3cf6a6050b9b6967b1bfa3202a61 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Mon, 7 Oct 2024 13:38:16 +0200 Subject: [PATCH 2/8] working --- conf/modules/annotate_svs.config | 4 +- conf/modules/call_svs.config | 2 +- nextflow.config | 2 +- nextflow_schema.json | 2 +- subworkflows/local/annotate_svs/main.nf | 2 + .../local/annotate_svs/tests/main.nf.test | 65 +++++--- .../annotate_svs/tests/main.nf.test.snap | 154 ++---------------- .../local/annotate_svs/tests/nextflow.config | 2 +- tests/nextflow.config | 2 +- 9 files changed, 67 insertions(+), 168 deletions(-) diff --git a/conf/modules/annotate_svs.config b/conf/modules/annotate_svs.config index 4e2d31c6..6a8d578d 100644 --- a/conf/modules/annotate_svs.config +++ b/conf/modules/annotate_svs.config @@ -32,7 +32,7 @@ process { '--appris --biotype --buffer_size 100 --canonical --cache --ccds', '--compress_output bgzip --distance 5000 --domains', '--exclude_predicted --force_overwrite --format vcf', - '--fork 4 --hgvs --humdiv --max_sv_size 248387328', + '--hgvs --humdiv --max_sv_size 248387328', '--no_progress --numbers --per_gene --polyphen p', '--protein --offline --sift p', // Add back regulatory with VEP 113 '--symbol --tsl --uniprot --vcf', @@ -46,7 +46,7 @@ process { ] } - withName: '.*ANNOTATE_SVS:TABIX_VEP' { + withName: '.*ANNOTATE_SVS:TABIX_ENSEMBLVEP_SV' { publishDir = [ path: { "${params.outdir}/svs/multi_sample/${meta.id}" }, mode: params.publish_dir_mode, diff --git a/conf/modules/call_svs.config b/conf/modules/call_svs.config index c5fdabe0..3e555119 100644 --- a/conf/modules/call_svs.config +++ b/conf/modules/call_svs.config @@ -57,7 +57,7 @@ process { publishDir = [ path: { "${params.outdir}/svs/multi_sample/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') || params.skip_sv_annotation ? null : filename } + saveAs: { filename -> filename.equals('versions.yml') || !params.skip_sv_annotation ? null : filename } ] } diff --git a/nextflow.config b/nextflow.config index d4fae7cf..63934d6e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -86,7 +86,7 @@ params { help_full = false show_hidden = false version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/' // Config options config_profile_name = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 6d155698..a104f284 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -245,7 +245,7 @@ "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/", + "default": "https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/", "hidden": true } } diff --git a/subworkflows/local/annotate_svs/main.nf b/subworkflows/local/annotate_svs/main.nf index 022f523f..d36286e8 100644 --- a/subworkflows/local/annotate_svs/main.nf +++ b/subworkflows/local/annotate_svs/main.nf @@ -15,6 +15,8 @@ workflow ANNOTATE_SVS { main: ch_versions = Channel.empty() + ch_sv_dbs.view() + ch_sv_dbs .map { meta, csv -> csv } .splitCsv ( header:true ) diff --git a/subworkflows/local/annotate_svs/tests/main.nf.test b/subworkflows/local/annotate_svs/tests/main.nf.test index c480ff89..cab1851b 100644 --- a/subworkflows/local/annotate_svs/tests/main.nf.test +++ b/subworkflows/local/annotate_svs/tests/main.nf.test @@ -11,32 +11,25 @@ nextflow_workflow { process { """ input[0] = [ - [ id:'test' ], + [ id:'hg38' ], file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true) ] """ } } - run("SAMTOOLS_FAIDX") { - script "../../../../modules/nf-core/samtools/faidx/main.nf" - process { - """ - input[0] = GUNZIP.out.gunzip - input[1] = [[],[]] - """ - } - } - run("SEVERUS") { script "../../../../modules/nf-core/severus/main" process { """ - input[0] = Channel.of([ + input[0] = [ [ id:'test', single_end:false, project: 'project' ], // meta map file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true) - )] + file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true), + [], + [], + [] + ] input[1] = [[],[]] """ } @@ -61,16 +54,17 @@ nextflow_workflow { when { workflow { """ - input[0] = SEVERUS.out.vcf + input[0] = SEVERUS.out.all_vcf input[1] = GUNZIP.out.gunzip input[2] = Channel.of([ + [ id: 'svdb_dbs' ], file(params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv', checkIfExists: true) ]) - input[4] = UNTAR.out.untar.map { meta, cache -> cache } - input[5] = Channel.value('110') - input[6] = [ + input[3] = UNTAR.out.untar.map { meta, cache -> cache } + input[4] = Channel.value('110') + input[5] = Channel.of([ file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true) - ] + ]) """ } } @@ -80,11 +74,42 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.versions, - path(workflow.out.vcf.get(0).get(1)), + path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5, file(workflow.out.tbi.get(0).get(1)).name ).match() } ) } } + + test("severus, fasta, svdb, vep_cache, '110', vep_plugins -stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = SEVERUS.out.all_vcf + input[1] = GUNZIP.out.gunzip + input[2] = Channel.of([ + [ id: 'svdb_dbs' ], + file(params.pipelines_testdata_base_path + 'testdata/svdb_dbs.csv', checkIfExists: true) + ]) + input[3] = UNTAR.out.untar.map { meta, cache -> cache } + input[4] = Channel.value('110') + input[5] = Channel.of([ + file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out.versions).match() } + ) + } + + } } diff --git a/subworkflows/local/annotate_svs/tests/main.nf.test.snap b/subworkflows/local/annotate_svs/tests/main.nf.test.snap index 2b09646f..1f02f6af 100644 --- a/subworkflows/local/annotate_svs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_svs/tests/main.nf.test.snap @@ -1,158 +1,30 @@ { - "bcf, db, vep_cache, '110', -stub": { + "severus, fasta, svdb, vep_cache, '110', vep_plugins -stub": { "content": [ [ - "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22", - "versions.yml:md5,992301857689684643c42695c032a7f2", - "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", - "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" - ], - [ - [ - { - "id": "test_data.bed", - "project": null, - "contains_affected": false - }, - "test_data.bed.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - [ - { - "id": "test_data.bed", - "project": null, - "contains_affected": false - }, - "test_data.bed.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "versions.yml:md5,84c59e3a0a183b01a21620b16ee9ca4d", + "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-09-19T10:33:26.596869783" + "timestamp": "2024-10-07T13:34:18.847540046" }, - "bcf, db, vep_cache, '110'": { + "severus, fasta, svdb, vep_cache, '110', vep_plugins": { "content": [ [ - "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22", - "versions.yml:md5,992301857689684643c42695c032a7f2", - "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", - "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" + "versions.yml:md5,84c59e3a0a183b01a21620b16ee9ca4d", + "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed" ], - "test_data.bed.vcf.gz.tbi", - [ - "##INFO=", - "##VEP-command-line='vep --assembly GRCh38 --cache --cache_version 110 --compress_output bgzip --database 0 --dir_cache [PATH]/vep_cache --fasta hg38.test.fa --fork 2 --input_file test_data.bed_filltags_anno.vcf.gz --offline --output_file test_data.bed.vcf.gz --vcf'", - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest", - "chr16\t63972\tchr16_63972_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000262316|protein_coding||3/17||||||||||-1||HGNC|HGNC:20561,C|intron_variant&NMD_transcript_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000417043|nonsense_mediated_decay||2/3||||||||||-1||HGNC|HGNC:20561,C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000419764|protein_coding||3/3||||||||||-1|cds_end_NF|HGNC|HGNC:20561,C|intron_variant&NMD_transcript_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000428730|nonsense_mediated_decay||2/16||||||||||-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000448893|protein_coding|||||||||||4210|-1|cds_start_NF|HGNC|HGNC:20561,C|intron_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000450643|protein_coding||3/4||||||||||-1|cds_end_NF|HGNC|HGNC:20561,C|downstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000472390|retained_intron|||||||||||580|-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000482904|retained_intron|||||||||||1766|-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000486045|retained_intron|||||||||||3779|-1||HGNC|HGNC:20561,C|non_coding_transcript_exon_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000487201|retained_intron|2/3||||1177|||||||-1||HGNC|HGNC:20561,C|upstream_gene_variant|MODIFIER|RHBDF1|ENSG00000007384|Transcript|ENST00000493647|retained_intron|||||||||||3292|-1||HGNC|HGNC:20561\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:11:20,11,0:..", - "chr16\t86889\tchr16_86889_T_C\tT\tC\t21\t.\tAF=1;AQ=21;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000219431|protein_coding|||||||||||1047|1||HGNC|HGNC:7211,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000356432|protein_coding|||||||||||1043|1||HGNC|HGNC:7211,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000397817|protein_coding|||||||||||1038|1||HGNC|HGNC:7211,C|intron_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000399953|protein_coding||11/11||||||||||-1||HGNC|HGNC:14124,C|downstream_gene_variant|MODIFIER|MPG|ENSG00000103152|Transcript|ENST00000436333|protein_coding|||||||||||1205|1|cds_end_NF|HGNC|HGNC:7211,C|upstream_gene_variant|MODIFIER||ENSG00000269482|Transcript|ENST00000601483|lncRNA|||||||||||3742|1|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000610509|retained_intron||1/2||||||||||-1||HGNC|HGNC:14124,C|intron_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000611875|protein_coding||13/13||||||||||-1||HGNC|HGNC:14124,C|intron_variant&NMD_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000621703|nonsense_mediated_decay||10/10||||||||||-1||HGNC|HGNC:14124,C|intron_variant&NMD_transcript_variant|MODIFIER|NPRL3|ENSG00000103148|Transcript|ENST00000622194|nonsense_mediated_decay||11/11||||||||||-1||HGNC|HGNC:14124\tGT:DP:AD:GQ:PL:RNC\t1/1:28:0,28:18:21,20,0:..", - "chr16\t160055\tchr16_160055_C_G\tC\tG\t18\t.\tAF=1;AQ=18;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3067|1||HGNC|HGNC:4836,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4427|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,29:17:18,22,0:..", - "chr16\t160070\tchr16_160070_C_CGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\tC\tCGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3051|1||HGNC|HGNC:4836,GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGACACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTGTGAGACGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGAGATGCCCAGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGTTTGAGAGGTGCCCGGGAT|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4411|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:8,7:2:9,0,18:..", - "chr16\t160089\tchr16_160089_TG_T\tTG\tT\t14\t.\tAF=0.5;AQ=14;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3032|1||HGNC|HGNC:4836,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4392|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:25,5:15:14,0,29:..", - "chr16\t160180\tchr16_160180_C_T\tC\tT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2942|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4302|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:29:1,28:15:15,25,0:..", - "chr16\t160216\tchr16_160216_T_A\tT\tA\t10\t.\tAF=1;AQ=10;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2906|1||HGNC|HGNC:4836,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4266|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,27:6:10,6,0:..", - "chr16\t160217\tchr16_160217_C_T\tC\tT\t9\t.\tAF=1;AQ=9;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2905|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4265|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:27:0,27:5:9,3,0:..", - "chr16\t160326\tchr16_160326_T_A\tT\tA\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2796|1||HGNC|HGNC:4836,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4156|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:0,29:14:15,18,0:..", - "chr16\t160327\tchr16_160327_C_T\tC\tT\t16\t.\tAF=1;AQ=16;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2795|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4155|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:29:3,26:14:16,17,0:..", - "chr16\t160388\tchr16_160388_G_GGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\tG\tGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\t15\t.\tAF=0.5;AQ=15;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2733|1||HGNC|HGNC:4836,GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4093|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:31:4,14:11:15,0,12:..", - "chr16\t160728\tchr16_160728_C_T\tC\tT\t5\t.\tAF=1;AQ=5;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2394|1||HGNC|HGNC:4836,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3754|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:30:8,22:4:5,3,0:..", - "chr16\t160746\tchr16_160746_T_C\tT\tC\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2376|1||HGNC|HGNC:4836,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3736|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:23,7:10:10,0,18:..", - "chr16\t160751\tchr16_160751_AG_A;chr16_160752_G_GGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\tAG\tA\t8\t.\tAF=0.5;AQ=8;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2370|1||HGNC|HGNC:4836,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3730|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/0:22:.,7:6:0,0,0:..", - "chr16\t160752\tchr16_160751_AG_A;chr16_160752_G_GGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\tG\tGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA\t8\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2369|1||HGNC|HGNC:4836,GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGA|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3729|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:.,14:6:0,0,0:..", - "chr16\t161210\tchr16_161210_GC_G\tGC\tG\t6\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1911|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4767|1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3271|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:27:21,5:7:6,0,27:..", - "chr16\t161474\tchr16_161474_TA_T\tTA\tT\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1647|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4503|1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3007|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:25:16,9:23:22,0,39:..", - "chr16\t162329\tchr16_162329_G_A\tG\tA\t23\t.\tAF=0.5;AQ=23;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||793|1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||3649|1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2153|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:24:23,0,41:..", - "chr16\t162650\tchr16_162650_C_T\tC\tT\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||472|1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||3328|1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1832|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:24:9,15:33:34,0,41:..", - "chr16\t163106\tchr16_163106_C_T\tC\tT\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||16|1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2872|1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1376|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:22:22,0,39:..", - "chr16\t163140\tchr16_163140_T_G\tT\tG\t17\t.\tAF=0.5;AQ=17;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|1/3||||19|||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2838|1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1342|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:17:17,0,39:..", - "chr16\t163143\tchr16_163143_G_A\tG\tA\t16\t.\tAF=0.5;AQ=16;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|1/3||||22|||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2835|1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1339|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:17:16,0,41:..", - "chr16\t163229\tchr16_163229_T_C\tT\tC\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2749|1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1253|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:23:15,8:3:0,0,27:..", - "chr16\t163796\tchr16_163796_T_A\tT\tA\t12\t.\tAF=1;AQ=12;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2182|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4883|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||686|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:15:0,15:7:12,7,0:..", - "chr16\t163800\tchr16_163800_G_A\tG\tA\t8\t.\tAF=1;AQ=8;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2178|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4879|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||682|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:16:2,14:3:8,0,0:..", - "chr16\t163804\tchr16_163804_G_A\tG\tA\t14\t.\tAF=1;AQ=14;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2174|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4875|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||678|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:13:14,16,0:..", - "chr16\t164431\tchr16_164431_T_TG\tT\tTG\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||1/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1546|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4247|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||50|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:22:25,25,0:..", - "chr16\t164541\tchr16_164541_G_GGTCC\tG\tGGTCC\t26\t.\tAF=0.5;AQ=26;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GTCC|non_coding_transcript_exon_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|2/3||||155-156|||||||1||HGNC|HGNC:4836,GTCC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1436|1||HGNC|HGNC:4826,GTCC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4137|1||HGNC|HGNC:4825,GTCC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GTCC|non_coding_transcript_exon_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|1/3||||60-61|||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:13,7:26:26,0,39:..", - "chr16\t164690\tchr16_164690_C_CGCGGGGCGCGGTGCGGGCGGG\tC\tCGCGGGGCGCGGTGCGGGCGGG\t27\t.\tAF=0.5;AQ=27;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGGGCGCGGTGCGGGCGGG|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGGGCGCGGTGCGGGCGGG|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1287|1||HGNC|HGNC:4826,GCGGGGCGCGGTGCGGGCGGG|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3988|1||HGNC|HGNC:4825,GCGGGGCGCGGTGCGGGCGGG|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGGGCGCGGTGCGGGCGGG|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:6,14:25:27,0,28:..", - "chr16\t164723\tchr16_164723_C_T\tC\tT\t11\t.\tAF=0.5;AQ=11;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1255|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3956|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:15,4:11:11,0,21:..", - "chr16\t164731\tchr16_164731_C_CG\tC\tCG\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1246|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3947|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:2,14:2:14,0,22:..", - "chr16\t164740\tchr16_164740_C_T\tC\tT\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1238|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3939|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:1,18:2:2,0,1:..", - "chr16\t164771\tchr16_164771_T_C\tT\tC\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1207|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3908|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:13,6:4:10,0,25:..", - "chr16\t164791\tchr16_164791_G_A\tG\tA\t16\t.\tAF=0.5;AQ=16;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1187|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3888|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:6,15:15:16,0,20:..", - "chr16\t164800\tchr16_164800_G_GGCGGGGTCGCGGGGCGGGGCGAGGTC\tG\tGGCGGGGTCGCGGGGCGGGGCGAGGTC\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGGGTCGCGGGGCGGGGCGAGGTC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1177|1||HGNC|HGNC:4826,GCGGGGTCGCGGGGCGGGGCGAGGTC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3878|1||HGNC|HGNC:4825,GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGGGTCGCGGGGCGGGGCGAGGTC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,4:5:4,0,19:..", - "chr16\t164817\tchr16_164817_C_A\tC\tA\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1161|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3862|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:8,13:21:22,0,27:..", - "chr16\t164831\tchr16_164831_C_CG\tC\tCG\t4\t.\tAF=1;AQ=4;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1146|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3847|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:4,15:2:4,0,0:..", - "chr16\t164839\tchr16_164839_G_GGT\tG\tGGT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GT|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1138|1||HGNC|HGNC:4826,GT|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3839|1||HGNC|HGNC:4825,GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GT|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:2,15:10:15,10,0:..", - "chr16\t164871\tchr16_164871_T_G\tT\tG\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1107|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3808|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:12,7:14:13,0,33:..", - "chr16\t164884\tchr16_164884_G_GT\tG\tGT\t15\t.\tAF=1;AQ=15;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1093|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3794|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:21:0,21:15:15,22,0:..", - "chr16\t164892\tchr16_164892_CG_C\tCG\tC\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1085|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3786|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:18,3:5:2,0,21:..", - "chr16\t164907\tchr16_164907_C_A\tC\tA\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1071|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3772|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:12,8:5:3,0,20:..", - "chr16\t164931\tchr16_164931_C_G\tC\tG\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1047|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3748|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:1,8:5:3,0,19:..", - "chr16\t164932\tchr16_164932_G_GGGCGGGC\tG\tGGGCGGGC\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GGCGGGC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1045|1||HGNC|HGNC:4826,GGCGGGC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3746|1||HGNC|HGNC:4825,GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGCGGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:2,7:4:1,0,15:..", - "chr16\t164942\tchr16_164942_G_GT\tG\tGT\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,T|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1035|1||HGNC|HGNC:4826,T|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3736|1||HGNC|HGNC:4825,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,T|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:9:0,8:6:4,0,14:..", - "chr16\t164953\tchr16_164953_G_GGCGGC\tG\tGGCGGC\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GCGGC|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1024|1||HGNC|HGNC:4826,GCGGC|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3725|1||HGNC|HGNC:4825,GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GCGGC|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,6:13:13,0,33:..", - "chr16\t164985\tchr16_164985_C_CG\tC\tCG\t18\t.\tAF=1;AQ=18;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,G|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||992|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3693|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t1/1:19:1,18:16:18,18,0:..", - "chr16\t165212\tchr16_165212_TC_T\tTC\tT\t3\t.\tAF=0.5;AQ=3;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||57|1||HGNC|HGNC:4836,-|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||765|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3466|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:18,3:5:3,0,30:..", - "chr16\t165380\tchr16_165380_G_A\tG\tA\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||224|1||HGNC|HGNC:4836,A|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||598|1||HGNC|HGNC:4826,A|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3299|1||HGNC|HGNC:4825,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,A|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,8:29:29,0,43:..", - "chr16\t165856\tchr16_165856_G_C\tG\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||700|1||HGNC|HGNC:4836,C|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||122|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2823|1||HGNC|HGNC:4825,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,C|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,8:29:29,0,44:..", - "chr16\t166191\tchr16_166191_C_CG\tC\tCG\t22\t.\tAF=0.5;AQ=22;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1035|1||HGNC|HGNC:4836,G|intron_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding||1/2||||||||||1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2487|1||HGNC|HGNC:4825,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,G|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:22:14,6:23:22,0,36:..", - "chr16\t166518\tchr16_166518_TG_T\tTG\tT\t11\t.\tAF=0.5;AQ=11;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||1363|1||HGNC|HGNC:4836,-|intron_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding||2/2||||||||||1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2160|1||HGNC|HGNC:4825,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||2/2||||||||||1||HGNC|HGNC:4826,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined||2/2||||||||||1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:16,4:12:11,0,32:..", - "chr16\t167928\tchr16_167928_GT_G\tGT\tG\t17\t.\tAF=0.5;AQ=17;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4947|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2773|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1165|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4961|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||750|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1168|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4965|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1168|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:14,6:17:17,0,31:..", - "chr16\t167947\tchr16_167947_T_TC\tT\tTC\t19\t.\tAF=0.5;AQ=19;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4928|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2791|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1183|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4942|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||731|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1186|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4946|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4996|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1186|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:21:11,10:18:19,0,22:..", - "chr16\t167948\tchr16_167948_T_C\tT\tC\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4928|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2792|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1184|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4942|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||731|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1187|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4946|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4996|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1187|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:20:10,10:10:10,0,17:..", - "chr16\t168533\tchr16_168533_T_C\tT\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4343|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3377|1||HGNC|HGNC:4836,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1769|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4357|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||146|1||HGNC|HGNC:4825,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1772|1||HGNC|HGNC:4826,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4361|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4411|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1772|1||HGNC|HGNC:4826,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4969|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:29:29,0,43:..", - "chr16\t168736\tchr16_168736_A_G\tA\tG\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||4140|1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3580|1||HGNC|HGNC:4836,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1972|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||4154|1||HGNC|HGNC:4824,G|non_coding_transcript_exon_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|1/3||||58|||||||1||HGNC|HGNC:4825,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||1975|1||HGNC|HGNC:4826,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||4158|1||HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4208|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||1975|1||HGNC|HGNC:4826,G|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4766|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:34:34,0,48:..", - "chr16\t169117\tchr16_169117_TG_T\tTG\tT\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3758|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||3962|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2354|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3772|1||HGNC|HGNC:4824,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2357|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3776|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3826|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2357|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4384|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:17,3:6:4,0,27:..", - "chr16\t169404\tchr16_169404_TC_T\tTC\tT\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3471|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||4249|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2641|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3485|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||71|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2644|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3489|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3539|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2644|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||4097|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:16,2:7:5,0,30:..", - "chr16\t169624\tchr16_169624_TC_T\tTC\tT\t10\t.\tAF=0.5;AQ=10;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3251|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||4469|1||HGNC|HGNC:4836,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||2861|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3265|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||291|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||2864|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3269|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3319|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||2864|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3877|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,4:11:10,0,32:..", - "chr16\t170831\tchr16_170831_T_TCACA\tT\tTCACA\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||2044|1||HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4067|1||HGNC|HGNC:4826,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||2058|1||HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1497|1||HGNC|HGNC:4825,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||2062|1||HGNC|HGNC:4824,CACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2112|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,CACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4070|1||HGNC|HGNC:4826,CACA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2670|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:6,6:3:19,0,25:..", - "chr16\t170862\tchr16_170862_C_CACACA\tC\tCACACA\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||2013|1||HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4098|1||HGNC|HGNC:4826,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||2027|1||HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1528|1||HGNC|HGNC:4825,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4101|1||HGNC|HGNC:4826,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||2031|1||HGNC|HGNC:4824,ACACA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2081|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,ACACA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4101|1||HGNC|HGNC:4826,ACACA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2639|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,2:7:5,0,28:..", - "chr16\t170943\tchr16_170943_AG_A\tAG\tA\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1932|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4180|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1946|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1610|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4183|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1950|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||2000|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4183|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2558|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:18,2:4:1,0,26:..", - "chr16\t171206\tchr16_171206_T_TTTA\tT\tTTTA\t13\t.\tAF=0.5;AQ=13;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4442|1||HGNC|HGNC:4826,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1683|1||HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1872|1||HGNC|HGNC:4825,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4445|1||HGNC|HGNC:4826,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1687|1||HGNC|HGNC:4824,TTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1737|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,TTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4445|1||HGNC|HGNC:4826,TTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2295|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:11,9:13:13,0,22:..", - "chr16\t171219\tchr16_171219_T_TTA\tT\tTTA\t1\t.\tAF=0.5;AQ=1;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1656|1||HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4455|1||HGNC|HGNC:4826,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1670|1||HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1885|1||HGNC|HGNC:4825,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4458|1||HGNC|HGNC:4826,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1674|1||HGNC|HGNC:4824,TA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1724|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,TA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4458|1||HGNC|HGNC:4826,TA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2282|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:14,3:4:1,0,20:..", - "chr16\t171220\tchr16_171220_T_TATTA\tT\tTATTA\t9\t.\tAF=0.5;AQ=9;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1655|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4456|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1669|1||HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||1886|1||HGNC|HGNC:4825,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1673|1||HGNC|HGNC:4824,ATTA|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1723|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,ATTA|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4459|1||HGNC|HGNC:4826,ATTA|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||2281|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:20:16,4:10:9,0,23:..", - "chr16\t171534\tchr16_171534_AT_A\tAT\tA\t20\t.\tAF=0.5;AQ=20;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||1341|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||4771|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1355|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2201|1||HGNC|HGNC:4825,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined|||||||||||4774|1||HGNC|HGNC:4826,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1359|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1409|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||4774|1||HGNC|HGNC:4826,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1967|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:14,5:20:20,0,40:..", - "chr16\t171881\tchr16_171881_TC_T\tTC\tT\t21\t.\tAF=0.5;AQ=21;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||994|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4798|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4822|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||1008|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2548|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4816|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||1012|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||1062|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4866|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1620|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:21:21,0,35:.." - ], - [ - "chr16\t172418\tchr16_172418_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||458|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4262|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4286|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||472|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3084|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4280|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||476|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||526|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4330|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4895|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1084|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:16:20,17,0:..", - "chr16\t172636\tchr16_172636_C_T\tC\tT\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||240|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4044|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4068|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||254|1||HGNC|HGNC:4824,T|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3302|1||HGNC|HGNC:4825,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4062|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||258|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||308|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4112|1||HGNC|HGNC:4823,T|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4677|-1|||,T|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||866|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:1,17:14:23,14,0:..", - "chr16\t172870\tchr16_172870_G_C\tG\tC\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||6|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||3810|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||3834|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||20|1||HGNC|HGNC:4824,C|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3536|1||HGNC|HGNC:4825,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||3828|1||HGNC|HGNC:4823,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||24|1||HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||74|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,C|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3878|1||HGNC|HGNC:4823,C|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4443|-1|||,C|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||632|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:18:0,18:20:24,22,0:..", - "chr16\t173116\tchr16_173116_TC_T\tTC\tT\t6\t.\tAF=0.5;AQ=6;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding||1/2||||||||||1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||3563|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||3587|1||HGNC|HGNC:4823,-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding||1/2||||||||||1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3783|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||3581|1||HGNC|HGNC:4823,-|non_coding_transcript_exon_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|1/2||||224|||||||1||HGNC|HGNC:4824,-|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding||1/1||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3631|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4196|-1|||,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||385|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:16,3:8:6,0,30:..", - "chr16\t173707\tchr16_173707_A_G\tA\tG\t27\t.\tAF=1;AQ=27;AC=2;cadd_raw=0.19;cadd_phred=3.05;CSQ=G|3_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|3/3||||573|||||||1||HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||2973|1||HGNC|HGNC:4823,G|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||4847|1||RFAM|,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||2997|1||HGNC|HGNC:4823,G|3_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|3/3||||510|||||||1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||4373|1||HGNC|HGNC:4825,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||2991|1||HGNC|HGNC:4823,G|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||32|1||HGNC|HGNC:4824,G|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||244|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,G|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3041|1||HGNC|HGNC:4823,G|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||3606|-1|||,G|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||47|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:19:0,19:25:27,27,0:..", - "chr16\t176848\tchr16_176848_GC_G\tGC\tG\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||3610|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3139|1||HGNC|HGNC:4824,-|intron_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding||1/2||||||||||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1705|1||RFAM|,-|intron_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding||1/2||||||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3139|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|1/2||||152|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3174|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3386|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|intron_variant&non_coding_transcript_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron||1/1||||||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||464|-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3189|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:15,2:6:5,0,28:..", - "chr16\t176953\tchr16_176953_CA_C\tCA\tC\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||3505|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3244|1||HGNC|HGNC:4824,-|frameshift_variant|HIGH|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|2/3||||158|121|41|K/X|Aag/ag|||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1600|1||RFAM|,-|frameshift_variant|HIGH|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|2/3||||85|25|9|K/X|Aag/ag|||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3244|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|1/2||||257|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3279|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||3491|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|2/2||||90|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||359|-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3294|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:15,2:7:5,0,30:..", - "chr16\t177485\tchr16_177485_AC_A\tAC\tA\t5\t.\tAF=0.5;AQ=5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBQ1|ENSG00000086506|Transcript|ENST00000199708|protein_coding|||||||||||2973|1||HGNC|HGNC:4833,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||3776|1||HGNC|HGNC:4824,-|3_prime_UTR_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|3/3||||541|||||||1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000207243|Transcript|ENST00000384514|misc_RNA|||||||||||1068|1||RFAM|,-|3_prime_UTR_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|3/3||||468|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||3776|1||HGNC|HGNC:4824,-|non_coding_transcript_exon_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|2/2||||640|||||||1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||3811|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||4023|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||212|1||HGNC|HGNC:4823,-|non_coding_transcript_exon_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|1/1||||5|||||||-1|||,-|upstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||3826|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:17:13,4:6:5,0,31:..", - "chr16\t274052\tchr16_274052_A_G\tA\tG\t28\t.\tAF=1;AQ=28;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|synonymous_variant&NMD_transcript_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000168869|nonsense_mediated_decay|5/15||||353|250|84|L|Tta/Cta|||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000301679|protein_coding|||||||||||3972|1||HGNC|HGNC:14163,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000316163|protein_coding|6/17||||434|357|119|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000359740|protein_coding|5/16||||387|387|129|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|synonymous_variant|LOW|RGS11|ENSG00000076344|Transcript|ENST00000397770|protein_coding|6/17||||453|420|140|D|gaT/gaC|||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000472466|retained_intron|||||||||||887|-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000477143|retained_intron|1/9||||905|||||||-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000481672|retained_intron|2/11||||110|||||||-1||HGNC|HGNC:9993,G|non_coding_transcript_exon_variant|MODIFIER|RGS11|ENSG00000076344|Transcript|ENST00000493449|retained_intron|5/9||||1199|||||||-1||HGNC|HGNC:9993,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000600536|nonsense_mediated_decay|||||||||||4109|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000653392|nonsense_mediated_decay|||||||||||4216|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000654053|nonsense_mediated_decay|||||||||||4154|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000659283|nonsense_mediated_decay|||||||||||1869|1||HGNC|HGNC:14163,G|downstream_gene_variant|MODIFIER|FAM234A|ENSG00000167930|Transcript|ENST00000666018|nonsense_mediated_decay|||||||||||4097|1||HGNC|HGNC:14163\tGT:DP:AD:GQ:PL:RNC\t1/1:32:0,32:26:28,29,0:..", - "chr16\t286660\tchr16_286660_G_A\tG\tA\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000219406|protein_coding|9/11||||1353|1347|449|T|acG/acA|||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000219409|protein_coding|||||||||||3650|1||HGNC|HGNC:680,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding|||||||||||780|-1||HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding|||||||||||781|-1||HGNC|HGNC:903,A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000404312|protein_coding|9/11||||1343|1338|446|T|acG/acA|||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000414650|protein_coding|||||||||||3850|1|cds_end_NF|HGNC|HGNC:680,A|synonymous_variant|LOW|PDIA2|ENSG00000185615|Transcript|ENST00000435833|protein_coding|3/5||||234|234|78|T|acG/acA|||1|cds_start_NF|HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000447871|protein_coding|||||||||||3972|1|cds_end_NF|HGNC|HGNC:680,A|downstream_gene_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000456379|protein_coding|||||||||||1520|1|cds_start_NF&cds_end_NF|HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000457798|protein_coding|||||||||||1530|-1|cds_start_NF|HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron|||||||||||780|-1||HGNC|HGNC:903,A|downstream_gene_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000462950|protein_coding_CDS_not_defined|||||||||||1084|1||HGNC|HGNC:14180,A|non_coding_transcript_exon_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000467212|retained_intron|8/10||||1418|||||||1||HGNC|HGNC:14180,A|downstream_gene_variant|MODIFIER|ARHGDIG|ENSG00000242173|Transcript|ENST00000477621|retained_intron|||||||||||3820|1||HGNC|HGNC:680,A|non_coding_transcript_exon_variant|MODIFIER|PDIA2|ENSG00000185615|Transcript|ENST00000482665|retained_intron|5/7||||1630|||||||1||HGNC|HGNC:14180\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:19:25,19,0:..", - "chr16\t309953\tchr16_309953_A_G\tA\tG\t33\t.\tAF=0.5;AQ=33;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding||4/10||||||||||-1||HGNC|HGNC:903,G|intron_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding||4/9||||||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron||3/7||||||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000481769|protein_coding_CDS_not_defined||3/4||||||||||-1||HGNC|HGNC:903\tGT:DP:AD:GQ:PL:RNC\t0/1:11:6,5:33:33,0,44:..", - "chr16\t346264\tchr16_346264_A_G\tA\tG\t31\t.\tAF=0.5;AQ=31;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|synonymous_variant|LOW|AXIN1|ENSG00000103126|Transcript|ENST00000262320|protein_coding|2/11||||1198|762|254|D|gaT/gaC|||-1||HGNC|HGNC:903,G|synonymous_variant|LOW|AXIN1|ENSG00000103126|Transcript|ENST00000354866|protein_coding|2/10||||924|762|254|D|gaT/gaC|||-1||HGNC|HGNC:903,G|non_coding_transcript_exon_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000461023|retained_intron|1/8||||59|||||||-1||HGNC|HGNC:903,G|intron_variant&non_coding_transcript_variant|MODIFIER|AXIN1|ENSG00000103126|Transcript|ENST00000481769|protein_coding_CDS_not_defined||1/4||||||||||-1||HGNC|HGNC:903\tGT:DP:AD:GQ:PL:RNC\t0/1:26:15,11:31:31,0,40:..", - "chr16\t377013\tchr16_377013_G_C\tG\tC\t28\t.\tAF=0.5;AQ=28;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000250930|protein_coding||4/12||||||||||-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000424078|protein_coding|||||||||||2162|-1|cds_start_NF|HGNC|HGNC:17205,C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000427313|protein_coding||4/4||||||||||-1|cds_end_NF|HGNC|HGNC:17205,C|intron_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000431232|protein_coding||4/12||||||||||-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000448854|protein_coding|||||||||||1798|-1|cds_start_NF|HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000467452|retained_intron|||||||||||1938|-1||HGNC|HGNC:17205,C|upstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000475348|retained_intron|||||||||||538|-1||HGNC|HGNC:17205,C|downstream_gene_variant|MODIFIER|PGAP6|ENSG00000129925|Transcript|ENST00000476735|protein_coding_CDS_not_defined|||||||||||95|-1||HGNC|HGNC:17205\tGT:DP:AD:GQ:PL:RNC\t0/1:17:11,6:29:28,0,42:..", - "chr16\t520623\tchr16_520623_G_A\tG\tA\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000262305|protein_coding||13/13||||||||||1||HGNC|HGNC:17224,A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000434585|protein_coding||14/14||||||||||1||HGNC|HGNC:17224,A|intron_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000450428|protein_coding||11/11||||||||||1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000461009|retained_intron|||||||||||1515|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000464263|retained_intron|||||||||||861|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|RAB11FIP3|ENSG00000090565|Transcript|ENST00000487899|retained_intron|||||||||||1605|1||HGNC|HGNC:17224,A|downstream_gene_variant|MODIFIER|LINC00235|ENSG00000277142|Transcript|ENST00000622160|lncRNA|||||||||||4532|-1||HGNC|HGNC:14138\tGT:DP:AD:GQ:PL:RNC\t0/1:18:9,9:34:34,0,44:..", - "chr16\t551632\tchr16_551632_T_C\tT\tC\t21\t.\tAF=1;AQ=21;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|synonymous_variant|LOW|CAPN15|ENSG00000103326|Transcript|ENST00000219611|protein_coding|9/14||||2820|2313|771|G|ggT/ggC|||1||HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000562370|protein_coding|||||||||||4240|1|cds_end_NF|HGNC|HGNC:11182,C|upstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000565010|retained_intron|||||||||||665|1||HGNC|HGNC:11182,C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000261691|Transcript|ENST00000565879|lncRNA||1/1||||||||||-1|||,C|upstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000566977|protein_coding|||||||||||1123|1|cds_start_NF|HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000568988|protein_coding|||||||||||3423|1|cds_end_NF|HGNC|HGNC:11182,C|downstream_gene_variant|MODIFIER|CAPN15|ENSG00000103326|Transcript|ENST00000637507|protein_coding|||||||||||3601|1|cds_end_NF|HGNC|HGNC:11182\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:15:21,16,0:..", - "chr16\t582180\tchr16_582180_G_C\tG\tC\t25\t.\tAF=1;AQ=25;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000026218|protein_coding||9/9||||||||||1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000321878|protein_coding||9/10||||||||||1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000409527|protein_coding||10/11||||||||||1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000420990|nonsense_mediated_decay||6/7||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000422307|protein_coding|||||||||||4946|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000443147|nonsense_mediated_decay||10/11||||||||||1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000470411|protein_coding|||||||||||4963|1||HGNC|HGNC:14135,C|non_coding_transcript_exon_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000476438|retained_intron|1/2||||420|||||||1||HGNC|HGNC:14135,C|intron_variant&non_coding_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000480424|retained_intron||3/4||||||||||1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000537901|retained_intron|||||||||||3378|1||HGNC|HGNC:14135,C|intron_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000540241|protein_coding||2/3||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000540548|protein_coding_CDS_not_defined|||||||||||310|1||HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000544860|protein_coding_CDS_not_defined|||||||||||3337|1||HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000634341|retained_intron|||||||||||697|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635205|nonsense_mediated_decay||3/4||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635909|nonsense_mediated_decay||8/9||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000635935|protein_coding_CDS_not_defined|||||||||||1403|1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000636005|nonsense_mediated_decay||8/9||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000636657|nonsense_mediated_decay||10/11||||||||||1||HGNC|HGNC:14135,C|intron_variant&NMD_transcript_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000637468|nonsense_mediated_decay||6/7||||||||||1|cds_start_NF|HGNC|HGNC:14135,C|downstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000638143|nonsense_mediated_decay|||||||||||1258|1|cds_start_NF|HGNC|HGNC:14135,C|upstream_gene_variant|MODIFIER|PIGQ|ENSG00000007541|Transcript|ENST00000638152|protein_coding_CDS_not_defined|||||||||||1404|1||HGNC|HGNC:14135\tGT:DP:AD:GQ:PL:RNC\t1/1:6:0,6:9:25,8,0:..", - "chr16\t627629\tchr16_627629_T_C\tT\tC\t20\t.\tAF=1;AQ=20;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000248139|protein_coding|6/6||||1079|||||||1||HGNC|HGNC:18285,C|upstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000319070|protein_coding|||||||||||3356|1||HGNC|HGNC:30912,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000509637|nonsense_mediated_decay|||||||||||1636|1|cds_start_NF|HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000535977|protein_coding|7/7||||1075|||||||1||HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000538492|protein_coding|7/7||||927|||||||1||HGNC|HGNC:18285,C|3_prime_UTR_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000539661|protein_coding|7/7||||967|||||||1||HGNC|HGNC:18285,C|non_coding_transcript_exon_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000561781|retained_intron|2/2||||796|||||||1||HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000563109|protein_coding|||||||||||46|1|cds_start_NF&cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000564703|protein_coding|||||||||||1512|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000565511|nonsense_mediated_decay|||||||||||1546|1||HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000566290|protein_coding|||||||||||214|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000568586|protein_coding|||||||||||1508|1|cds_end_NF|HGNC|HGNC:18285,C|downstream_gene_variant|MODIFIER|RAB40C|ENSG00000197562|Transcript|ENST00000569575|protein_coding|||||||||||1603|1|cds_end_NF|HGNC|HGNC:18285,C|upstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000573440|retained_intron|||||||||||1610|1||HGNC|HGNC:30912\tGT:DP:AD:GQ:PL:RNC\t1/1:13:0,13:13:20,13,0:..", - "chr16\t638557\tchr16_638557_A_C\tA\tC\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000301686|protein_coding|||||||||||2252|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000307650|protein_coding|||||||||||3271|1||HGNC|HGNC:14142,C|downstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000319070|protein_coding|||||||||||4440|1||HGNC|HGNC:30912,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000338401|protein_coding|||||||||||2215|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397664|protein_coding|||||||||||2206|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397665|protein_coding|||||||||||2267|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000397666|protein_coding|||||||||||2255|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000448973|retained_intron|||||||||||2247|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000456420|nonsense_mediated_decay|||||||||||2318|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000474840|nonsense_mediated_decay|||||||||||3372|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000491999|nonsense_mediated_decay|||||||||||3289|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000564039|nonsense_mediated_decay|||||||||||2279|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000565163|protein_coding|||||||||||2297|-1|cds_start_NF&cds_end_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000565799|retained_intron|||||||||||2290|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568077|nonsense_mediated_decay|||||||||||2226|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568773|protein_coding|||||||||||2322|-1|cds_start_NF|HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000568830|protein_coding|||||||||||2199|-1|cds_end_NF|HGNC|HGNC:14141,C|downstream_gene_variant|MODIFIER|WFIKKN1|ENSG00000127578|Transcript|ENST00000573440|retained_intron|||||||||||4441|1||HGNC|HGNC:30912,C|intron_variant&non_coding_transcript_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000611328|protein_coding_CDS_not_defined||1/3||||||||||1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|METTL26|ENSG00000130731|Transcript|ENST00000614890|protein_coding|||||||||||2191|-1||HGNC|HGNC:14141,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000615744|protein_coding_CDS_not_defined|||||||||||3894|1||HGNC|HGNC:14142,C|non_coding_transcript_exon_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000619114|protein_coding_CDS_not_defined|2/2||||576|||||||1||HGNC|HGNC:14142,C|non_coding_transcript_exon_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000619377|protein_coding_CDS_not_defined|2/2||||664|||||||1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000620462|retained_intron|||||||||||3926|1||HGNC|HGNC:14142,C|upstream_gene_variant|MODIFIER|MCRIP2|ENSG00000172366|Transcript|ENST00000629534|protein_coding|||||||||||3292|1||HGNC|HGNC:14142\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:16:24,17,0:..", - "chr16\t655844\tchr16_655844_T_C\tT\tC\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000293879|protein_coding|17/41||||1973|1921|641|L|Ttg/Ctg|||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000420061|retained_intron|17/17||||1985|||||||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546516|retained_intron|3/20||||614|||||||1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547407|retained_intron|||||||||||431|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548844|protein_coding_CDS_not_defined|||||||||||2716|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548859|retained_intron|||||||||||589|1||HGNC|HGNC:26960,C|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000549091|protein_coding|17/41||||2013|1921|641|L|Ttg/Ctg|||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000549648|retained_intron|17/17||||1988|||||||1||HGNC|HGNC:26960,C|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000550593|retained_intron|||||||||||2374|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000550739|protein_coding|||||||||||3401|1|cds_start_NF&cds_end_NF|HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552648|protein_coding_CDS_not_defined|4/7||||455|||||||1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552683|retained_intron|||||||||||2014|1||HGNC|HGNC:26960,C|upstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552728|nonsense_mediated_decay|||||||||||577|1|cds_start_NF|HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552943|retained_intron|15/26||||3591|||||||1||HGNC|HGNC:26960,C|non_coding_transcript_exon_variant|MODIFIER||ENSG00000262528|Transcript|ENST00000573609|lncRNA|1/2||||351|||||||-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:16:23,17,0:..", - "chr16\t667523\tchr16_667523_G_T\tG\tT\t27\t.\tAF=1;AQ=27;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000293879|protein_coding|41/41||||5233|5181|1727|P|ccG/ccT|||1||HGNC|HGNC:26960,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000315082|protein_coding|||||||||||609|1||HGNC|HGNC:21169,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000315764|protein_coding|6/6||||1147|834|278|P|ccG/ccT|||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546516|retained_intron|||||||||||4090|1||HGNC|HGNC:26960,T|missense_variant|MODERATE|WDR90|ENSG00000161996|Transcript|ENST00000546896|protein_coding|2/2||||89|89|30|R/L|cGt/cTt|||1|cds_start_NF|HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000546923|retained_intron|||||||||||4787|1||HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547407|retained_intron|24/24||||3541|||||||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000547543|protein_coding_CDS_not_defined|||||||||||778|1||HGNC|HGNC:26960,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000547944|protein_coding|7/7||||1365|978|326|P|ccG/ccT|||1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548448|retained_intron|||||||||||1162|1||HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000548603|protein_coding_CDS_not_defined|||||||||||4086|1||HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000549024|retained_intron|12/12||||1951|||||||1||HGNC|HGNC:26960,T|synonymous_variant|LOW|WDR90|ENSG00000161996|Transcript|ENST00000549091|protein_coding|41/41||||5279|5187|1729|P|ccG/ccT|||1||HGNC|HGNC:26960,T|3_prime_UTR_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000551100|protein_coding|3/3||||315|||||||1|cds_start_NF|HGNC|HGNC:26960,T|downstream_gene_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552683|retained_intron|||||||||||4085|1||HGNC|HGNC:26960,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000552728|nonsense_mediated_decay|22/22||||2826|||||||1|cds_start_NF|HGNC|HGNC:26960,T|non_coding_transcript_exon_variant|MODIFIER|WDR90|ENSG00000161996|Transcript|ENST00000553080|retained_intron|6/6||||1635|||||||1||HGNC|HGNC:26960,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561711|retained_intron|||||||||||4394|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561929|protein_coding|||||||||||686|1|cds_start_NF&cds_end_NF|HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000561983|nonsense_mediated_decay|||||||||||582|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562333|nonsense_mediated_decay|||||||||||664|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562598|retained_intron|||||||||||659|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000562708|retained_intron|||||||||||589|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563134|protein_coding|||||||||||583|1|cds_end_NF|HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563637|nonsense_mediated_decay|||||||||||628|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000563776|retained_intron|||||||||||582|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000565004|retained_intron|||||||||||3559|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000566214|nonsense_mediated_decay|||||||||||628|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000566965|retained_intron|||||||||||1037|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000567017|retained_intron|||||||||||639|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000567589|retained_intron|||||||||||3005|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000568636|retained_intron|||||||||||1135|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000568950|retained_intron|||||||||||655|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569358|retained_intron|||||||||||2932|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569675|retained_intron|||||||||||612|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569706|retained_intron|||||||||||609|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000569943|protein_coding_CDS_not_defined|||||||||||830|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000570092|retained_intron|||||||||||601|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000570280|nonsense_mediated_decay|||||||||||630|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000602564|retained_intron|||||||||||657|1||HGNC|HGNC:21169,T|upstream_gene_variant|MODIFIER|RHOT2|ENSG00000140983|Transcript|ENST00000697194|protein_coding|||||||||||577|1||HGNC|HGNC:21169\tGT:DP:AD:GQ:PL:RNC\t1/1:22:0,22:23:27,24,0:..", - "chr16\t690466\tchr16_690466_A_G\tA\tG\t26\t.\tAF=1;AQ=26;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000248142|protein_coding|||||||||||22|-1||HGNC|HGNC:20852,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000293883|protein_coding|||||||||||68|-1||HGNC|HGNC:20852,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000397621|protein_coding|||||||||||2034|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562563|protein_coding|||||||||||2461|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562585|protein_coding_CDS_not_defined|||||||||||4192|-1||HGNC|HGNC:14150,G|downstream_gene_variant|MODIFIER|FBXL16|ENSG00000127585|Transcript|ENST00000562648|retained_intron|||||||||||2032|-1||HGNC|HGNC:14150,G|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000261659|Transcript|ENST00000566927|lncRNA||1/1||||||||||1|||,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000567014|retained_intron|||||||||||3537|-1||HGNC|HGNC:20852,G|non_coding_transcript_exon_variant|MODIFIER||ENSG00000261659|Transcript|ENST00000575305|retained_intron|1/1||||1466|||||||1|||,G|upstream_gene_variant|MODIFIER|WDR24|ENSG00000127580|Transcript|ENST00000647644|protein_coding|||||||||||219|-1||HGNC|HGNC:20852\tGT:DP:AD:GQ:PL:RNC\t1/1:17:0,17:20:26,21,0:..", - "chr16\t723341\tchr16_723341_G_A\tG\tA\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000219535|protein_coding|||||||||||768|1||HGNC|HGNC:14152,A|intron_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000293889|protein_coding||11/13||||||||||-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000341413|protein_coding|||||||||||3617|1||HGNC|HGNC:14177,A|intron_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000345165|protein_coding||11/13||||||||||-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000389701|retained_intron|||||||||||4064|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000389703|protein_coding|||||||||||3765|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000423653|protein_coding_CDS_not_defined|||||||||||1586|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000439619|retained_intron|||||||||||1209|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000460023|retained_intron|||||||||||1566|-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000463539|retained_intron||9/11||||||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000466708|retained_intron||10/12||||||||||-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000471861|retained_intron|||||||||||1660|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000474647|retained_intron|||||||||||1782|-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000478979|retained_intron|4/4||||2296|||||||-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000481804|retained_intron|4/5||||2627|||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000482152|retained_intron||3/4||||||||||-1||HGNC|HGNC:14153,A|non_coding_transcript_exon_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000482878|retained_intron|4/4||||2699|||||||-1||HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000485091|retained_intron||10/11||||||||||-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000538176|retained_intron|||||||||||1201|-1||HGNC|HGNC:14153,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000544996|retained_intron|||||||||||1643|-1||HGNC|HGNC:14153,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000549114|protein_coding|||||||||||3595|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000561546|protein_coding|||||||||||3905|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000561750|retained_intron|||||||||||3934|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000562141|protein_coding|||||||||||3778|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000562187|protein_coding|||||||||||3765|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000563792|protein_coding|||||||||||4398|1|cds_end_NF|HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000564000|protein_coding|||||||||||756|1||HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000564537|protein_coding|||||||||||3765|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000564545|protein_coding|||||||||||3921|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000564640|retained_intron|||||||||||1029|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000566437|retained_intron|||||||||||833|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000566525|retained_intron|||||||||||752|1||HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000567414|protein_coding|||||||||||3952|1|cds_end_NF|HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000567696|retained_intron|||||||||||3977|1||HGNC|HGNC:14177,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000568141|protein_coding|||||||||||4005|1|cds_end_NF|HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|METRN|ENSG00000103260|Transcript|ENST00000568223|protein_coding|||||||||||3686|1||HGNC|HGNC:14151,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000568916|protein_coding|||||||||||751|1|cds_start_NF|HGNC|HGNC:14152,A|upstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000569143|retained_intron|||||||||||3977|1||HGNC|HGNC:14177,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000569529|protein_coding|||||||||||751|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|ANTKMT|ENSG00000103254|Transcript|ENST00000570237|retained_intron|||||||||||751|1||HGNC|HGNC:14152,A|downstream_gene_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000650995|protein_coding|||||||||||2453|-1|cds_end_NF|HGNC|HGNC:14153,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCDC78|ENSG00000162004|Transcript|ENST00000682391|retained_intron||7/9||||||||||-1||HGNC|HGNC:14153\tGT:DP:AD:GQ:PL:RNC\t1/1:17:0,17:19:23,21,0:..", - "chr16\t739761\tchr16_739761_A_G\tA\tG\t22\t.\tAF=1;AQ=22;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000251588|protein_coding||1/10||||||||||-1||HGNC|HGNC:14179,G|5_prime_UTR_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000540986|protein_coding|1/10||||1174|||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000562421|protein_coding|||||||||||2006|-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000562752|retained_intron||1/4||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000563534|protein_coding_CDS_not_defined|||||||||||2297|-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565065|nonsense_mediated_decay||2/5||||||||||-1||HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565341|retained_intron||1/3||||||||||-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565425|nonsense_mediated_decay||1/9||||||||||-1||HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000565693|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14179,G|intron_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000566614|protein_coding||1/4||||||||||-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567172|protein_coding_CDS_not_defined||1/1||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567403|protein_coding|||||||||||2009|-1|cds_end_NF|HGNC|HGNC:14179,G|intron_variant&non_coding_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000567455|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14179,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000568545|protein_coding|||||||||||1872|-1||HGNC|HGNC:14179,G|downstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000569604|protein_coding_CDS_not_defined|||||||||||4236|1||HGNC|HGNC:14177,G|upstream_gene_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000569759|protein_coding_CDS_not_defined|||||||||||3391|-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000570066|nonsense_mediated_decay||1/4||||||||||-1||HGNC|HGNC:14179,G|intron_variant&NMD_transcript_variant|MODIFIER|CIAO3|ENSG00000103245|Transcript|ENST00000570289|nonsense_mediated_decay||1/3||||||||||-1||HGNC|HGNC:14179,G|downstream_gene_variant|MODIFIER|HAGHL|ENSG00000103253|Transcript|ENST00000647875|protein_coding_CDS_not_defined|||||||||||4408|1||HGNC|HGNC:14177\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:14:22,14,0:..", - "chr16\t766294\tchr16_766294_T_G\tT\tG\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000382862|protein_coding||11/16||||||||||1||HGNC|HGNC:7371,G|upstream_gene_variant|MODIFIER|MIR662|ENSG00000207579|Transcript|ENST00000384847|miRNA|||||||||||3889|1||HGNC|HGNC:32918,G|downstream_gene_variant|MODIFIER|MSLNL|ENSG00000162006|Transcript|ENST00000543963|protein_coding|||||||||||3134|-1|cds_start_NF|HGNC|HGNC:14170,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000545450|protein_coding||12/17||||||||||1||HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000561896|protein_coding||2/6||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000563651|protein_coding||10/10||||||||||1|cds_end_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000563941|protein_coding||12/17||||||||||1||HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000566269|protein_coding||2/7||||||||||1|cds_start_NF|HGNC|HGNC:7371,G|intron_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000566549|protein_coding||11/16||||||||||1||HGNC|HGNC:7371,G|downstream_gene_variant|MODIFIER|MSLN|ENSG00000102854|Transcript|ENST00000569566|protein_coding|||||||||||1258|1|cds_end_NF|HGNC|HGNC:7371,G|downstream_gene_variant|MODIFIER||ENSG00000279136|Transcript|ENST00000623562|TEC|||||||||||2825|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:12,7:29:29,0,43:..", - "chr16\t789996\tchr16_789996_T_C\tT\tC\t36\t.\tAF=0.5;AQ=36;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000007264|protein_coding|||||||||||1615|-1||HGNC|HGNC:14173,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000262315|protein_coding||4/21||||||||||1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000317063|protein_coding||4/21||||||||||1||HGNC|HGNC:18435,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|CHTF18|ENSG00000127586|Transcript|ENST00000426047|protein_coding||2/6||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:18435,C|intron_variant&NMD_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000440239|nonsense_mediated_decay||4/13||||||||||1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000455171|protein_coding||3/20||||||||||1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000461268|protein_coding_CDS_not_defined|||||||||||2528|1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000464728|retained_intron||3/17||||||||||1||HGNC|HGNC:18435,C|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|CHTF18|ENSG00000127586|Transcript|ENST00000471202|retained_intron||4/18||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000479976|retained_intron||4/6||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000484349|retained_intron||1/3||||||||||1||HGNC|HGNC:18435,C|intron_variant&non_coding_transcript_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000491530|protein_coding_CDS_not_defined||2/5||||||||||1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000493715|protein_coding_CDS_not_defined|||||||||||4706|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000561734|protein_coding|||||||||||2015|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000562070|protein_coding|||||||||||2527|-1|cds_start_NF|HGNC|HGNC:14173,C|downstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000563545|nonsense_mediated_decay|||||||||||360|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000563560|protein_coding|||||||||||1667|-1|cds_end_NF|HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565377|protein_coding|||||||||||1615|-1|cds_end_NF|HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565503|nonsense_mediated_decay|||||||||||1656|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000565787|retained_intron|||||||||||1141|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000565809|protein_coding|||||||||||1625|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000567114|protein_coding|||||||||||1599|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000567283|nonsense_mediated_decay|||||||||||1663|-1||HGNC|HGNC:14173,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000567620|retained_intron|||||||||||703|1||HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000569270|nonsense_mediated_decay|||||||||||255|1|cds_start_NF|HGNC|HGNC:18435,C|upstream_gene_variant|MODIFIER|RPUSD1|ENSG00000007376|Transcript|ENST00000569601|protein_coding|||||||||||1662|-1|cds_end_NF|HGNC|HGNC:14173,C|downstream_gene_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000570058|protein_coding_CDS_not_defined|||||||||||656|1||HGNC|HGNC:18435,C|intron_variant|MODIFIER|CHTF18|ENSG00000127586|Transcript|ENST00000631357|protein_coding||5/23||||||||||1||HGNC|HGNC:18435\tGT:DP:AD:GQ:PL:RNC\t0/1:15:7,8:36:36,0,49:..", - "chr16\t813336\tchr16_813336_T_C\tT\tC\t32\t.\tAF=0.5;AQ=32;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER||ENSG00000287855|Transcript|ENST00000655150|lncRNA|||||||||||4153|1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:14:5,9:32:32,0,39:..", - "chr16\t893361\tchr16_893361_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||4/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||5/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||6/7||||||||||-1||HGNC|HGNC:14154,C|upstream_gene_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000565198|retained_intron|||||||||||109|-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding||3/5||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||3/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||4/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||4/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,45:..", - "chr16\t947473\tchr16_947473_T_C\tT\tC\t29\t.\tAF=0.5;AQ=29;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||2/10||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||2/11||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||2/7||||||||||-1||HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding||2/3||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|5_prime_UTR_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566627|protein_coding|1/6||||172|||||||-1|cds_end_NF|HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||2/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||2/9||||||||||-1||HGNC|HGNC:14154,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||2/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||2/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154\tGT:DP:AD:GQ:PL:RNC\t0/1:23:8,15:30:29,0,47:..", - "chr16\t964119\tchr16_964119_A_G\tA\tG\t24\t.\tAF=1;AQ=24;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000262301|protein_coding||1/10||||||||||-1||HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000543238|protein_coding||1/7||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000562226|nonsense_mediated_decay||1/7||||||||||-1||HGNC|HGNC:14154,G|missense_variant|MODERATE|LMF1|ENSG00000103227|Transcript|ENST00000562380|protein_coding|1/4||||4|4|2|Y/H|Tat/Cat|||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant&non_coding_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000566609|protein_coding_CDS_not_defined||1/2||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000567595|nonsense_mediated_decay||1/4||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568897|protein_coding||1/9||||||||||-1||HGNC|HGNC:14154,G|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000568964|nonsense_mediated_decay||1/5||||||||||-1|cds_start_NF|HGNC|HGNC:14154,G|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,G|downstream_gene_variant|MODIFIER||ENSG00000276931|Transcript|ENST00000620075|lncRNA|||||||||||4256|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:29:0,29:21:24,24,0:..", - "chr16\t977069\tchr16_977069_T_C\tT\tC\t34\t.\tAF=0.5;AQ=34;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=C|upstream_gene_variant|MODIFIER|SOX8|ENSG00000005513|Transcript|ENST00000293894|protein_coding|||||||||||4701|1||HGNC|HGNC:11203,C|intron_variant&NMD_transcript_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000545827|nonsense_mediated_decay||1/11||||||||||-1||HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000562570|lncRNA|2/2||||1914|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563837|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000563863|lncRNA|4/4||||423|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565069|lncRNA|3/3||||265|||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565139|lncRNA|||||||||||143|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000565467|lncRNA||1/1||||||||||-1||HGNC|HGNC:53928,C|upstream_gene_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000567961|lncRNA|||||||||||157|-1||HGNC|HGNC:53928,C|intron_variant&non_coding_transcript_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000568394|lncRNA||1/2||||||||||-1||HGNC|HGNC:53928,C|intron_variant|MODIFIER|LMF1|ENSG00000103227|Transcript|ENST00000570014|protein_coding||1/6||||||||||-1|cds_end_NF|HGNC|HGNC:14154,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000655952|lncRNA|3/3||||743|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000662104|lncRNA|3/3||||322|||||||-1||HGNC|HGNC:53928,C|non_coding_transcript_exon_variant|MODIFIER|CEROX1|ENSG00000260807|Transcript|ENST00000669274|lncRNA|3/3||||225|||||||-1||HGNC|HGNC:53928\tGT:DP:AD:GQ:PL:RNC\t0/1:17:6,11:34:34,0,44:.." - ] + "28e9be031273d5e4a94a8654da6e56ed", + "test_svs_annotated.vcf.gz.tbi" ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-08-12T10:10:59.241809478" + "timestamp": "2024-10-07T13:32:21.970341761" } } \ No newline at end of file diff --git a/subworkflows/local/annotate_svs/tests/nextflow.config b/subworkflows/local/annotate_svs/tests/nextflow.config index aceda89d..862966e9 100644 --- a/subworkflows/local/annotate_svs/tests/nextflow.config +++ b/subworkflows/local/annotate_svs/tests/nextflow.config @@ -4,7 +4,7 @@ process { ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' } } - withName: 'ENSEMBLVEP_SV' { + withName: 'ANNOTATE_SVS:ENSEMBLVEP_SV' { ext.args = { [ '--offline', '--vcf', diff --git a/tests/nextflow.config b/tests/nextflow.config index 5d15b433..5e0b8fd0 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -3,7 +3,7 @@ params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' // Base directory for genomic-medicine-sweden/nallo test data - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/' max_cpus = 4 max_memory = '15.GB' From afd110dfdd66a30badfcc6ccf5d210b1cd18d02a Mon Sep 17 00:00:00 2001 From: fellen31 Date: Mon, 7 Oct 2024 14:32:25 +0200 Subject: [PATCH 3/8] fix snv annotation --- .../local/snv_annotation/tests/main.nf.test.snap | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test.snap b/subworkflows/local/snv_annotation/tests/main.nf.test.snap index 43fa52a6..be278f54 100644 --- a/subworkflows/local/snv_annotation/tests/main.nf.test.snap +++ b/subworkflows/local/snv_annotation/tests/main.nf.test.snap @@ -2,10 +2,10 @@ "bcf, db, vep_cache, '110', -stub": { "content": [ [ + "versions.yml:md5,1c67249781a135b3abbc3c7e63af4d0b", "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22", - "versions.yml:md5,992301857689684643c42695c032a7f2", - "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", - "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" + "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533", + "versions.yml:md5,f533675b4401f25d7dcfc9f63abeb619" ], [ [ @@ -32,15 +32,15 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T10:33:26.596869783" + "timestamp": "2024-10-07T14:29:17.858999735" }, "bcf, db, vep_cache, '110'": { "content": [ [ + "versions.yml:md5,1c67249781a135b3abbc3c7e63af4d0b", "versions.yml:md5,503122d4650f6a8a39b4e810063d6c22", - "versions.yml:md5,992301857689684643c42695c032a7f2", - "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", - "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" + "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533", + "versions.yml:md5,f533675b4401f25d7dcfc9f63abeb619" ], "test_data.bed.vcf.gz.tbi", "ad2f3def07bee1f4bab9cfe456dada3e", From a8207e215070a9326248479fdfc64d77e004f897 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Mon, 7 Oct 2024 18:30:12 +0200 Subject: [PATCH 4/8] docs and split --- CITATIONS.md | 4 ++ conf/modules/call_svs.config | 5 -- conf/modules/general.config | 26 ++++++++- docs/output.md | 16 ++++++ docs/parameters.md | 29 ++++++++++ docs/usage.md | 10 +++- subworkflows/local/annotate_svs/main.nf | 2 - .../local/utils_nfcore_nallo_pipeline/main.nf | 6 ++ tests/main.nf.test | 20 +++---- workflows/nallo.nf | 55 ++++++++++++------- 10 files changed, 135 insertions(+), 38 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 21c4c141..5128c352 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -110,6 +110,10 @@ > Nilsson D, Magnusson M. moonso/stranger v0.7.1. Published online February 18, 2021. doi:10.5281/ZENODO.4548873 +- [SVDB](https://github.com/J35P312/SVDB) + + > Eisfeldt et al., 2017. + - [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743) > Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011;27(5):718-719. doi:10.1093/bioinformatics/btq671 diff --git a/conf/modules/call_svs.config b/conf/modules/call_svs.config index 3e555119..35d80ef2 100644 --- a/conf/modules/call_svs.config +++ b/conf/modules/call_svs.config @@ -67,10 +67,5 @@ process { '--output-type z', '--write-index=tbi' ].join(' ') - publishDir = [ - path: { "${params.outdir}/svs/single_sample/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/general.config b/conf/modules/general.config index 28752027..12cbee2a 100644 --- a/conf/modules/general.config +++ b/conf/modules/general.config @@ -57,7 +57,7 @@ process { ] } - withName: '.*:NALLO:BCFTOOLS_PLUGINSPLIT' { + withName: '.*:NALLO:BCFTOOLS_PLUGINSPLIT_SNVS' { ext.args = [ '-i \'GT="alt"\'', '--output-type z', @@ -81,6 +81,30 @@ process { ] } + withName: '.*:NALLO:BCFTOOLS_PLUGINSPLIT_SVS' { + ext.args = [ + '-i \'GT="alt"\'', + '--output-type z', + '--write-index=tbi' + ].join(' ') + publishDir = [ + path: { "${params.outdir}/svs/single_sample/" }, + mode: params.publish_dir_mode, + // Can't use prefix as it would come from the original file + saveAs: { filename -> + if (filename.equals('versions.yml')) { + null + } else { + def matcher = filename =~ /(.+)(\.vcf\.gz(?:\.tbi)?)$/ + def sample = matcher[0][1] + def extension = matcher[0][2] + def annotated = params.skip_sv_annotation ? "" : "_annotated" + "${sample}/${sample}_svs${annotated}${extension}" + } + } + ] + } + withName: '.*:NALLO:SAMPLESHEET_PED' { publishDir = [ enabled: false diff --git a/docs/output.md b/docs/output.md index 3a457b0e..0f41b938 100644 --- a/docs/output.md +++ b/docs/output.md @@ -27,6 +27,7 @@ - [Ranking](#ranking) - [Ranked Variants](#ranked-variants) - [SV Calling](#sv-calling) + - [SV Annotation](#sv-annotation) ## Pipeline overview @@ -348,3 +349,18 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - `*.vcf.gz`: VCF with variants per sample - `*.vcf.gz.tbi`: Index of the corresponding VCF file + +### SV Annotation + +[SVDB](https://github.com/J35P312/SVDB) and [VEP](https://www.ensembl.org/vep) are used to annotate SVs. + +
+Output files from SV Annotation + +- `{outputdir}/svs/multi_sample/{project}` + - `{project}_svs_annotated.vcf.gz`: VCF file with annotated merged variants + - `{project}_svs_annotated.vcf.gz.tbi`: Index of the corresponding VCF file +- `{outputdir}/svs/single_sample/{sample}` + - `*.vcf_annotated.gz`: VCF with annotated variants per sample + - `*.vcf_annotated.gz.tbi`: Index of the corresponding VCF file +
diff --git a/docs/parameters.md b/docs/parameters.md index 1aa07374..938f3518 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -17,6 +17,7 @@ Allows skipping certain parts of the pipeline | `skip_repeat_annotation` | Skip tandem repeat annotation | `boolean` | False | | | | `skip_phasing_wf` | Skip phasing of variants and haplotagging of reads | `boolean` | False | | | | `skip_snv_annotation` | Skip short variant annotation | `boolean` | False | | | +| `skip_sv_annotation` | Skip structural variant annotation | `boolean` | False | | | | `skip_cnv_calling` | Skip CNV calling | `boolean` | False | | | | `skip_call_paralogs` | Skip the calling of specific paralogous genes | `boolean` | False | | | | `skip_rank_variants` | Skip ranking of short variants | `boolean` | False | | | @@ -109,3 +110,31 @@ Workflow options specific to genomic-medicine-sweden/nallo | `extra_vep_options` | Extra options to VEP, used for test profile. | `string` | | | True | | `extra_paraphase_options` | Extra options to Paraphase, used for test profile. | `string` | | | True | | `extra_hifiasm_options` | Extra options to hifiasm, used for test profile. | `string` | | | True | + +## File inputs + +The different files that are required. Some are only required by certain workflows, see the usage documentation. + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `cadd_prescored` | Path to a directory containing prescored indels for CADD.
HelpThis folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
| `string` | | | | +| `cadd_resources` | Path to a directory containing CADD annotations.
HelpThis folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
| `string` | | | | +| `par_regions` | Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant | `string` | | | | +| `tandem_repeats` | A tandem repeat BED file for sniffles | `string` | | | | +| `trgt_repeats` | A BED file with repeats to be genotyped with TRGT | `string` | | | | +| `snp_db` | A csv file with echtvar databases to annotate SNVs with | `string` | | | | +| `svdb_dbs` | Databases used for structural variant annotation in vcf format.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| `string` | | | | +| `variant_catalog` | A variant catalog json-file for stranger | `string` | | | | +| `variant_consequences_snv` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html | `string` | | | | +| `vep_cache` | A path to the VEP cache location | `string` | | | | +| `bed` | A BED file with regions of interest, used to limit short variant calling. | `string` | | | | +| `hificnv_xy` | A BED file containing expected copy number regions for XY samples. | `string` | | | | +| `hificnv_xx` | A BED file containing expected copy number regions for XX samples. | `string` | | | | +| `hificnv_exclude` | A BED file specifying regions to exclude with HiFiCNV, such as centromeres. | `string` | | | | +| `reduced_penetrance` | A file with gene ids that have reduced penetrance. For use with genmod. | `string` | | | | +| `score_config_snv` | A SNV rank model config file for genmod. | `string` | | | | +| `somalier_sites` | A VCF of known polymorphic sites for somalier | `string` | | | | +| `validationFailUnrecognisedParams` | Validation of parameters fails when an unrecognised parameter is found.
HelpBy default, when an unrecognised parameter is found, it returns a warning.
| `boolean` | | | True | +| `validationLenientMode` | Validation of parameters in lenient more.
HelpAllows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode).
| `boolean` | | | True | +| `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/ | | True | +>>>>>>> d3a25c2 (docs and split) diff --git a/docs/usage.md b/docs/usage.md index ff2b2fda..846e5701 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -236,9 +236,17 @@ cadd,/path/to/cadd.v1.6.hg38.zip > [!NOTE] > Optionally, to calcuate CADD scores for small indels, supply a path to a folder containing cadd annotations with `--cadd_resources` and prescored indels with `--cadd_prescored`. Equivalent of the `data/annotations/` and `data/prescored/` folders described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation). CADD scores for SNVs can be annotated through echvtvar and `--snp_db`. +### SV annotation (`--skip_sv_annotation`) + +This subworkflow relies on the mapping subworkflow, and requires the following additional files: + +| Parameter | Description | +| ---------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `svdb_dbs` | Databases used for structural variant annotation in vcf format.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| + ### Rank variants (`--skip_rank_variants`) -This subworkflow relies on the mapping, short variant calling and SNV annotation subworkflows, and requires the following additional files: +This subworkflow ranks SNVs and INDELs, and relies on the mapping, short variant calling and SNV annotation subworkflows, and requires the following additional files: | Parameter | Description | | -------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | diff --git a/subworkflows/local/annotate_svs/main.nf b/subworkflows/local/annotate_svs/main.nf index d36286e8..022f523f 100644 --- a/subworkflows/local/annotate_svs/main.nf +++ b/subworkflows/local/annotate_svs/main.nf @@ -15,8 +15,6 @@ workflow ANNOTATE_SVS { main: ch_versions = Channel.empty() - ch_sv_dbs.view() - ch_sv_dbs .map { meta, csv -> csv } .splitCsv ( header:true ) diff --git a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf index 0291099f..d40c8791 100644 --- a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf @@ -365,6 +365,12 @@ def toolCitationText() { "GLnexus (Yun et al. 2021)", ] } + if (!params.skip_sv_annotation) { + citation_text = citation_text + [ + "VEP (McLaren et al. 2016)", + "SVDB (Eisfeldt et al. 2017)", + ] + } if (!params.skip_snv_annotation) { citation_text = citation_text + [ "CADD (Rentzsch et al. 2019, Rentzsch et al. 2021)", diff --git a/tests/main.nf.test b/tests/main.nf.test index de6147be..35fac2da 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -110,8 +110,8 @@ nextflow_pipeline { { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_spanning_sorted.bam.bai").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_Revio/HG002_Revio_snv_annotated_ranked.vcf.gz").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_Revio/HG002_Revio_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_Revio/HG002_Revio_severus.vcf.gz").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_Revio/HG002_Revio_severus.vcf.gz.tbi").exists() } + { assert new File("$outputDir/svs/single_sample/HG002_Revio/HG002_Revio_svs_annotated.vcf.gz").exists() }, + { assert new File("$outputDir/svs/single_sample/HG002_Revio/HG002_Revio_svs_annotated.vcf.gz.tbi").exists() } ) } } @@ -261,8 +261,8 @@ nextflow_pipeline { { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_spanning_sorted.bam.bai").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_Revio_A/HG002_Revio_A_snv_annotated_ranked.vcf.gz").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_Revio_A/HG002_Revio_A_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_Revio_A/HG002_Revio_A_severus.vcf.gz").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_Revio_A/HG002_Revio_A_severus.vcf.gz.tbi").exists() }, + { assert new File("$outputDir/svs/single_sample/HG002_Revio_A/HG002_Revio_A_svs_annotated.vcf.gz").exists() }, + { assert new File("$outputDir/svs/single_sample/HG002_Revio_A/HG002_Revio_A_svs_annotated.vcf.gz.tbi").exists() }, // Assert exists HG002_Revio_B { assert new File("$outputDir/aligned_reads/HG002_Revio_B/HG002_Revio_B_haplotagged.bam.bai").exists() }, { assert new File("$outputDir/assembly_variant_calling/dipcall/HG002_Revio_B/HG002_Revio_B.hap1.bam.bai").exists() }, @@ -294,8 +294,8 @@ nextflow_pipeline { { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_spanning_sorted.bam.bai").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_Revio_B/HG002_Revio_B_snv_annotated_ranked.vcf.gz").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_Revio_B/HG002_Revio_B_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_Revio_B/HG002_Revio_B_severus.vcf.gz").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_Revio_B/HG002_Revio_B_severus.vcf.gz.tbi").exists() } + { assert new File("$outputDir/svs/single_sample/HG002_Revio_B/HG002_Revio_B_svs_annotated.vcf.gz").exists() }, + { assert new File("$outputDir/svs/single_sample/HG002_Revio_B/HG002_Revio_B_svs_annotated.vcf.gz.tbi").exists() } ) } } @@ -400,8 +400,8 @@ nextflow_pipeline { { assert new File("$outputDir/qc/fastqc/HG002_ONT_A/HG002_ONT_A_fastqc.zip").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_ONT_A/HG002_ONT_A_snv_annotated_ranked.vcf.gz").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_ONT_A/HG002_ONT_A_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_ONT_A/HG002_ONT_A_severus.vcf.gz").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_ONT_A/HG002_ONT_A_severus.vcf.gz.tbi").exists() }, + { assert new File("$outputDir/svs/single_sample/HG002_ONT_A/HG002_ONT_A_svs_annotated.vcf.gz").exists() }, + { assert new File("$outputDir/svs/single_sample/HG002_ONT_A/HG002_ONT_A_svs_annotated.vcf.gz.tbi").exists() }, // Assert exists HG002_ONT_B { assert new File("$outputDir/aligned_reads/HG002_ONT_B/HG002_ONT_B_haplotagged.bam.bai").exists() }, { assert new File("$outputDir/cnv_calling/hificnv/HG002_ONT_B/HG002_ONT_B.log").exists() }, @@ -426,8 +426,8 @@ nextflow_pipeline { { assert new File("$outputDir/qc/fastqc/HG002_ONT_B/HG002_ONT_B_fastqc.zip").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_ONT_B/HG002_ONT_B_snv_annotated_ranked.vcf.gz").exists() }, { assert new File("$outputDir/snvs/single_sample/HG002_ONT_B/HG002_ONT_B_snv_annotated_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_ONT_B/HG002_ONT_B_severus.vcf.gz").exists() }, - { assert new File("$outputDir/svs/single_sample/HG002_ONT_B/HG002_ONT_B_severus.vcf.gz.tbi").exists() } + { assert new File("$outputDir/svs/single_sample/HG002_ONT_B/HG002_ONT_B_svs_annotated.vcf.gz").exists() }, + { assert new File("$outputDir/svs/single_sample/HG002_ONT_B/HG002_ONT_B_svs_annotated.vcf.gz.tbi").exists() } ) } } diff --git a/workflows/nallo.nf b/workflows/nallo.nf index 79c47956..1bb4d50c 100644 --- a/workflows/nallo.nf +++ b/workflows/nallo.nf @@ -33,23 +33,24 @@ include { SNV_ANNOTATION } from '../subworkflows/local/ */ // local -include { CREATE_PEDIGREE_FILE as SAMPLESHEET_PED } from '../modules/local/create_pedigree_file/main' -include { CREATE_PEDIGREE_FILE as SOMALIER_PED } from '../modules/local/create_pedigree_file/main' -include { ECHTVAR_ENCODE } from '../modules/local/echtvar/encode/main' -include { SAMTOOLS_MERGE } from '../modules/nf-core/samtools/merge/main' +include { CREATE_PEDIGREE_FILE as SAMPLESHEET_PED } from '../modules/local/create_pedigree_file/main' +include { CREATE_PEDIGREE_FILE as SOMALIER_PED } from '../modules/local/create_pedigree_file/main' +include { ECHTVAR_ENCODE } from '../modules/local/echtvar/encode/main' +include { SAMTOOLS_MERGE } from '../modules/nf-core/samtools/merge/main' // nf-core -include { BCFTOOLS_CONCAT } from '../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_PLUGINSPLIT } from '../modules/nf-core/bcftools/pluginsplit/main' -include { BCFTOOLS_SORT } from '../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_STATS } from '../modules/nf-core/bcftools/stats/main' -include { MINIMAP2_ALIGN } from '../modules/nf-core/minimap2/align/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { SPLITUBAM } from '../modules/nf-core/splitubam/main' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nallo_pipeline' +include { BCFTOOLS_CONCAT } from '../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_PLUGINSPLIT as BCFTOOLS_PLUGINSPLIT_SNVS } from '../modules/nf-core/bcftools/pluginsplit/main' +include { BCFTOOLS_PLUGINSPLIT as BCFTOOLS_PLUGINSPLIT_SVS } from '../modules/nf-core/bcftools/pluginsplit/main' +include { BCFTOOLS_SORT } from '../modules/nf-core/bcftools/sort/main' +include { BCFTOOLS_STATS } from '../modules/nf-core/bcftools/stats/main' +include { MINIMAP2_ALIGN } from '../modules/nf-core/minimap2/align/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { SPLITUBAM } from '../modules/nf-core/splitubam/main' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nallo_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -313,7 +314,9 @@ workflow NALLO { ) ch_versions = ch_versions.mix(CALL_SVS.out.versions) - + CALL_SVS.out.ch_multisample_vcf + .join( CALL_SVS.out.ch_multisample_tbi ) + .set { ch_split_svs_in } // // Annotate structural variants // @@ -326,8 +329,22 @@ workflow NALLO { params.vep_cache_version, ch_vep_extra_files ) + + ANNOTATE_SVS.out.vcf + .join( ANNOTATE_SVS.out.tbi ) + .set { ch_split_svs_in } } + // Split the multisample SV VCF to also publish an (annotated) VCF per sample + BCFTOOLS_PLUGINSPLIT_SVS ( + ch_split_svs_in, + [], + [], + [], + [] + ) + ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSPLIT_SVS.out.versions) + // // Call (and annotate and rank) SNVs // @@ -440,10 +457,10 @@ workflow NALLO { ch_versions = ch_versions.mix(ECHTVAR_ENCODE.out.versions) // Split multisample VCF to also publish a VCF per sample - BCFTOOLS_PLUGINSPLIT ( BCFTOOLS_SORT.out.vcf.join(BCFTOOLS_SORT.out.tbi ), [], [], [], [] ) - ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSPLIT.out.versions) + BCFTOOLS_PLUGINSPLIT_SNVS ( BCFTOOLS_SORT.out.vcf.join(BCFTOOLS_SORT.out.tbi ), [], [], [], [] ) + ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSPLIT_SNVS.out.versions) - BCFTOOLS_PLUGINSPLIT.out.vcf + BCFTOOLS_PLUGINSPLIT_SNVS.out.vcf .transpose() .map { meta, vcf -> [ meta, vcf, [] ] } .set { ch_bcftools_stats_snv_in } From 00f48d26a86560845faaf7da4ce51c20e3fbf767 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Tue, 8 Oct 2024 08:58:11 +0200 Subject: [PATCH 5/8] update docs --- README.md | 1 + docs/usage.md | 17 +++++++++++++---- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index f170c7c1..4dd88d57 100644 --- a/README.md +++ b/README.md @@ -46,6 +46,7 @@ - Annotate SNVs and INDELs with databases of choice, i.e. [gnomAD](https://gnomad.broadinstitute.org), [CADD](https://cadd.gs.washington.edu) etc. with [echtvar](https://github.com/brentp/echtvar) and [VEP](https://github.com/Ensembl/ensembl-vep) - Annotate repeat expansions with [stranger](https://github.com/Clinical-Genomics/stranger) +- Annotate SVs with [SVDB](https://github.com/J35P312/SVDB) and [VEP](https://github.com/Ensembl/ensembl-vep) ##### Ranking diff --git a/docs/usage.md b/docs/usage.md index 846e5701..dadf1238 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -240,13 +240,22 @@ cadd,/path/to/cadd.v1.6.hg38.zip This subworkflow relies on the mapping subworkflow, and requires the following additional files: -| Parameter | Description | -| ---------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `svdb_dbs` | Databases used for structural variant annotation in vcf format.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| +| Parameter | Description | +| ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | +| `svdb_dbs` 1 | Csv file with databases used for structural variant annotation in vcf format.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| + +1 Example file for input with `--svdb_dbs`: + +``` +filename,in_freq_info_key,in_allele_count_info_key,out_freq_info_key,out_allele_count_info_key +https://github.com/genomic-medicine-sweden/test-datasets/raw/b9ff54b59cdd39df5b6e278a30b08d94075a644c/reference/colorsdb.test_data.vcf.gz,AF,AC,colorsdb_af,colorsdb_ac +``` + +These databases could for example come from [CoLoRSdb](https://zenodo.org/records/13145123). ### Rank variants (`--skip_rank_variants`) -This subworkflow ranks SNVs and INDELs, and relies on the mapping, short variant calling and SNV annotation subworkflows, and requires the following additional files: +This subworkflow ranks SNVs, and relies on the mapping, short variant calling and SNV annotation subworkflows, and requires the following additional files: | Parameter | Description | | -------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | From 402f2760d638ca1bca5b60fc964285a178b77901 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Fri, 11 Oct 2024 07:16:26 +0200 Subject: [PATCH 6/8] add back regulatory --- .nf-core.yml | 1 + assets/svdb_query_vcf_schema.json | 2 +- conf/modules/annotate_svs.config | 2 +- conf/test.config | 19 ++++++++++--------- docs/parameters.md | 31 ++----------------------------- tests/nextflow.config | 15 ++++++--------- 6 files changed, 21 insertions(+), 49 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index e3cc3de9..8a98a163 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -10,6 +10,7 @@ lint: - .github/workflows/awstest.yml - .github/workflows/awsfulltest.yml - conf/modules.config + - conf/igenomes_ignored.config files_unchanged: - CODE_OF_CONDUCT.md - assets/nf-core-nallo_logo_light.png diff --git a/assets/svdb_query_vcf_schema.json b/assets/svdb_query_vcf_schema.json index 0bb8540a..a927a1f3 100644 --- a/assets/svdb_query_vcf_schema.json +++ b/assets/svdb_query_vcf_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json", "title": "Schema for SVDB query - VCF", "description": "Schema for the SVDB query database input, VCF version", diff --git a/conf/modules/annotate_svs.config b/conf/modules/annotate_svs.config index 6a8d578d..dfed2cfd 100644 --- a/conf/modules/annotate_svs.config +++ b/conf/modules/annotate_svs.config @@ -34,7 +34,7 @@ process { '--exclude_predicted --force_overwrite --format vcf', '--hgvs --humdiv --max_sv_size 248387328', '--no_progress --numbers --per_gene --polyphen p', - '--protein --offline --sift p', // Add back regulatory with VEP 113 + '--protein --offline --sift p --regulatory', '--symbol --tsl --uniprot --vcf', '--no_stats' ].join(' ') } diff --git a/conf/test.config b/conf/test.config index 7f095770..5da8c4c7 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,14 +10,6 @@ ---------------------------------------------------------------------------------------- */ -process { - resourceLimits = [ - cpus: 4, - memory: '15.GB', - time: '1.h' - ] -} - params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' @@ -60,7 +52,7 @@ params { // Impose same minimum Nextflow version as in nextflow.config manifest { - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=24.04.2' } // Disable all Nextflow reporting options @@ -70,16 +62,25 @@ trace { enabled = false } dag { enabled = false } process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] withLabel: 'process_high' { cpus = 4 + memory = '15.GB' } withLabel: 'process_medium' { cpus = 2 + memory = '7.GB' } withLabel: 'process_low' { cpus = 1 + memory = '3.GB' } withLabel: 'process_single' { cpus = 1 + memory = '3.GB' } } diff --git a/docs/parameters.md b/docs/parameters.md index 938f3518..13164921 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -38,6 +38,7 @@ Define where the pipeline should find input data and save output data. | `tandem_repeats` | A tandem repeat BED file for sniffles | `string` | | | | | `trgt_repeats` | A BED file with repeats to be genotyped with TRGT | `string` | | | | | `snp_db` | A csv file with echtvar databases to annotate SNVs with | `string` | | | | +| `svdb_dbs` | Databases used for structural variant annotation in vcf format.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| `string` | | | | | `variant_catalog` | A variant catalog json-file for stranger | `string` | | | | | `variant_consequences_snv` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html | `string` | | | | | `vep_cache` | A path to the VEP cache location | `string` | | | | @@ -48,7 +49,7 @@ Define where the pipeline should find input data and save output data. | `reduced_penetrance` | A file with gene ids that have reduced penetrance. For use with genmod. | `string` | | | | | `score_config_snv` | A SNV rank model config file for genmod. | `string` | | | | | `somalier_sites` | A VCF of known polymorphic sites for somalier | `string` | | | | -| `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/1f4e062926fc10f70a38e917e5771edb333e89bf/ | | True | +| `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/ | | True | ## Reference genome options @@ -110,31 +111,3 @@ Workflow options specific to genomic-medicine-sweden/nallo | `extra_vep_options` | Extra options to VEP, used for test profile. | `string` | | | True | | `extra_paraphase_options` | Extra options to Paraphase, used for test profile. | `string` | | | True | | `extra_hifiasm_options` | Extra options to hifiasm, used for test profile. | `string` | | | True | - -## File inputs - -The different files that are required. Some are only required by certain workflows, see the usage documentation. - -| Parameter | Description | Type | Default | Required | Hidden | -|-----------|-----------|-----------|-----------|-----------|-----------| -| `cadd_prescored` | Path to a directory containing prescored indels for CADD.
HelpThis folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
| `string` | | | | -| `cadd_resources` | Path to a directory containing CADD annotations.
HelpThis folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
| `string` | | | | -| `par_regions` | Provide a bed file of chrX and chrY PAR regions for dipcall and DeepVariant | `string` | | | | -| `tandem_repeats` | A tandem repeat BED file for sniffles | `string` | | | | -| `trgt_repeats` | A BED file with repeats to be genotyped with TRGT | `string` | | | | -| `snp_db` | A csv file with echtvar databases to annotate SNVs with | `string` | | | | -| `svdb_dbs` | Databases used for structural variant annotation in vcf format.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| `string` | | | | -| `variant_catalog` | A variant catalog json-file for stranger | `string` | | | | -| `variant_consequences_snv` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html | `string` | | | | -| `vep_cache` | A path to the VEP cache location | `string` | | | | -| `bed` | A BED file with regions of interest, used to limit short variant calling. | `string` | | | | -| `hificnv_xy` | A BED file containing expected copy number regions for XY samples. | `string` | | | | -| `hificnv_xx` | A BED file containing expected copy number regions for XX samples. | `string` | | | | -| `hificnv_exclude` | A BED file specifying regions to exclude with HiFiCNV, such as centromeres. | `string` | | | | -| `reduced_penetrance` | A file with gene ids that have reduced penetrance. For use with genmod. | `string` | | | | -| `score_config_snv` | A SNV rank model config file for genmod. | `string` | | | | -| `somalier_sites` | A VCF of known polymorphic sites for somalier | `string` | | | | -| `validationFailUnrecognisedParams` | Validation of parameters fails when an unrecognised parameter is found.
HelpBy default, when an unrecognised parameter is found, it returns a warning.
| `boolean` | | | True | -| `validationLenientMode` | Validation of parameters in lenient more.
HelpAllows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode).
| `boolean` | | | True | -| `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/ | | True | ->>>>>>> d3a25c2 (docs and split) diff --git a/tests/nextflow.config b/tests/nextflow.config index 5e0b8fd0..f0408182 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -5,14 +5,11 @@ params { // Base directory for genomic-medicine-sweden/nallo test data pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/7be7114cb132be8cae9343f225bcf42ec11ecc1b/' - max_cpus = 4 - max_memory = '15.GB' - max_time = '6.h' } // Impose same minimum Nextflow version as the pipeline for testing manifest { - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=24.04.2' } // Disable all Nextflow reporting options @@ -22,25 +19,25 @@ trace { enabled = false } dag { enabled = false } process { - + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] withLabel: 'process_high' { cpus = 4 memory = '15.GB' } - withLabel: 'process_medium' { cpus = 2 memory = '7.GB' } - withLabel: 'process_low' { cpus = 1 memory = '3.GB' } - withLabel: 'process_single' { cpus = 1 memory = '3.GB' } - } From cda8f370df4e7a030317719f145f8a251c154210 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Fri, 11 Oct 2024 10:48:00 +0200 Subject: [PATCH 7/8] review suggestions --- modules.json | 227 +++++++++++++----- modules/nf-core/svdb/build/environment.yml | 5 - modules/nf-core/svdb/build/main.nf | 48 ---- modules/nf-core/svdb/build/meta.yml | 38 --- modules/nf-core/svdb/build/tests/main.nf.test | 111 --------- .../svdb/build/tests/main.nf.test.snap | 94 -------- modules/nf-core/svdb/build/tests/tags.yml | 2 - subworkflows/local/annotate_svs/main.nf | 3 +- .../annotate_svs/tests/main.nf.test.snap | 18 +- 9 files changed, 178 insertions(+), 368 deletions(-) delete mode 100644 modules/nf-core/svdb/build/environment.yml delete mode 100644 modules/nf-core/svdb/build/main.nf delete mode 100644 modules/nf-core/svdb/build/meta.yml delete mode 100644 modules/nf-core/svdb/build/tests/main.nf.test delete mode 100644 modules/nf-core/svdb/build/tests/main.nf.test.snap delete mode 100644 modules/nf-core/svdb/build/tests/tags.yml diff --git a/modules.json b/modules.json index 39279d5d..eab3a75b 100644 --- a/modules.json +++ b/modules.json @@ -8,271 +8,370 @@ "bcftools/annotate": { "branch": "master", "git_sha": "682f789f93070bd047868300dd018faf3d434e7c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "99a7e61b359f7b7b379cee49259879942d2d2533", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/pluginsplit": { "branch": "master", "git_sha": "c5abf7acbb2943bf09f4025cacbbcc2bc2292637", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/query": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/stats": { "branch": "master", "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cadd": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "deepvariant": { "branch": "master", "git_sha": "a7e8b8afd4fa82f20d745fa778bfdbf39c1f7efb", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "fastqc": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gawk": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "genmod/annotate": { "branch": "master", "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "genmod/compound": { "branch": "master", "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "genmod/models": { "branch": "master", "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "genmod/score": { "branch": "master", "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gfastats": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "glnexus": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hifiasm": { "branch": "master", "git_sha": "aecb06fcdb995ff3e3df7c7a1fd119367d6d1996", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "longphase/haplotag": { "branch": "master", "git_sha": "22fc6d90be8eca2cf6afe5d10b3c5cffcdbcb19c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "longphase/phase": { "branch": "master", "git_sha": "22fc6d90be8eca2cf6afe5d10b3c5cffcdbcb19c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "minimap2/align": { "branch": "master", "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "minimap2/index": { "branch": "master", "git_sha": "72e277acfd9e61a9f1368eafb4a9e83f5bcaa9f5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "modkit/pileup": { "branch": "master", "git_sha": "e29c9dda946de3c4d310d0b3f75664f0f3d5a842", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "paraphase": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/fastq": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/import": { "branch": "master", "git_sha": "90b63cde0f838ca4da3a88a37a5309888cae97b9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "e9bc33485e420b51cfbed3cf63ac7463cd5739d3", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/sort": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "severus": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sniffles": { "branch": "master", "git_sha": "b50aa17b1b604c7b3cfe58a2472d1e7b990ae8bf", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/sniffles/sniffles.diff" }, "somalier/extract": { "branch": "master", "git_sha": "458c882987320e27fc90723ec96c127a243a5497", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/somalier/extract/somalier-extract.diff" }, "somalier/relate": { "branch": "master", "git_sha": "458c882987320e27fc90723ec96c127a243a5497", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "splitubam": { "branch": "master", "git_sha": "d12bb6cdcd22ef8f26803a6a55e918ac017176e8", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stranger": { "branch": "master", "git_sha": "4806239588f35d27a95b187b4000d80e15152022", - "installed_by": ["modules"] - }, - "svdb/build": { - "branch": "master", - "git_sha": "ba8aac9d0b2f34811800bafab168b638cf2ff3cc", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/query": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgzip": { "branch": "master", "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/untar/untar.diff" } } @@ -282,20 +381,26 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/svdb/build/environment.yml b/modules/nf-core/svdb/build/environment.yml deleted file mode 100644 index cd35cf48..00000000 --- a/modules/nf-core/svdb/build/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::svdb=2.8.1 diff --git a/modules/nf-core/svdb/build/main.nf b/modules/nf-core/svdb/build/main.nf deleted file mode 100644 index db3055e2..00000000 --- a/modules/nf-core/svdb/build/main.nf +++ /dev/null @@ -1,48 +0,0 @@ -process SVDB_BUILD { - tag "$meta.id" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/svdb:2.8.1--py39h5371cbf_0': - 'biocontainers/svdb:2.8.1--py39h5371cbf_0' }" - - input: - tuple val(meta), path(input) - val(input_type) - - output: - tuple val(meta), path("*.db"), emit: db - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - if (!input_type.matches('folder|files')) { error "Unrecognised input type. Options are: 'folder', 'files'" } - - """ - svdb \\ - --build \\ - --$input_type $input \\ - --prefix ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.db - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/svdb/build/meta.yml b/modules/nf-core/svdb/build/meta.yml deleted file mode 100644 index c5c5a992..00000000 --- a/modules/nf-core/svdb/build/meta.yml +++ /dev/null @@ -1,38 +0,0 @@ -name: svdb_build -description: Build a structural variant database -keywords: - - structural variants - - build - - svdb -tools: - - svdb: - description: structural variant database software - homepage: https://github.com/J35P312/SVDB - documentation: https://github.com/J35P312/SVDB/blob/master/README.md - licence: ["MIT"] - -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input VCF file(s) or folder - pattern: "*" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - db: - type: file - description: SVDB database -authors: - - "@fellen31" diff --git a/modules/nf-core/svdb/build/tests/main.nf.test b/modules/nf-core/svdb/build/tests/main.nf.test deleted file mode 100644 index ccf18f2b..00000000 --- a/modules/nf-core/svdb/build/tests/main.nf.test +++ /dev/null @@ -1,111 +0,0 @@ -nextflow_process { - - name "Test Process SVDB_BUILD" - script "modules/nf-core/svdb/build/main.nf" - process "SVDB_BUILD" - tag "modules" - tag "modules_nfcore" - tag "svdb" - tag "svdb/build" - - test("one VCF - files") { - - when { - process { - """ - input[0] = Channel.of([ [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] - ]) - input[1] = 'files' - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot( - file(process.out.db.get(0).get(1)).name, - process.out.versions - ).match() } - ) - } - } - - test("two VCFs - files") { - - when { - process { - """ - input[0] = Channel.of([ [ id:'test' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true) - ] - ]) - input[1] = 'files' - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot( - file(process.out.db.get(0).get(1)).name, - process.out.versions - ).match() } - ) - } - } - - test("one VCF - files -stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] - ]) - input[1] = 'files' - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("two VCFs - files -stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ [ id:'test' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true) - ] - ]) - input[1] = 'files' - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - -} diff --git a/modules/nf-core/svdb/build/tests/main.nf.test.snap b/modules/nf-core/svdb/build/tests/main.nf.test.snap deleted file mode 100644 index 9a992957..00000000 --- a/modules/nf-core/svdb/build/tests/main.nf.test.snap +++ /dev/null @@ -1,94 +0,0 @@ -{ - "one VCF - files": { - "content": [ - "test.db", - [ - "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-18T11:37:21.374511177" - }, - "two VCFs - files": { - "content": [ - "test.db", - [ - "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-18T11:37:27.968892336" - }, - "two VCFs - files -stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" - ], - "db": [ - [ - { - "id": "test" - }, - "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-18T11:40:04.558825564" - }, - "one VCF - files -stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" - ], - "db": [ - [ - { - "id": "test" - }, - "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-18T10:54:45.735248435" - } -} \ No newline at end of file diff --git a/modules/nf-core/svdb/build/tests/tags.yml b/modules/nf-core/svdb/build/tests/tags.yml deleted file mode 100644 index 7eb9b2ab..00000000 --- a/modules/nf-core/svdb/build/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -svdb/query: - - modules/nf-core/svdb/build/** diff --git a/subworkflows/local/annotate_svs/main.nf b/subworkflows/local/annotate_svs/main.nf index 022f523f..14ed7ed7 100644 --- a/subworkflows/local/annotate_svs/main.nf +++ b/subworkflows/local/annotate_svs/main.nf @@ -36,7 +36,8 @@ workflow ANNOTATE_SVS { ch_svdb_in.out_frqs.toList(), ch_svdb_in.vcf_dbs.toList(), [] - ) + ) + ch_versions = ch_versions.mix(SVDB_QUERY.out.versions) ENSEMBLVEP_SV ( SVDB_QUERY.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] }, diff --git a/subworkflows/local/annotate_svs/tests/main.nf.test.snap b/subworkflows/local/annotate_svs/tests/main.nf.test.snap index 1f02f6af..0e7c747d 100644 --- a/subworkflows/local/annotate_svs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_svs/tests/main.nf.test.snap @@ -3,28 +3,30 @@ "content": [ [ "versions.yml:md5,84c59e3a0a183b01a21620b16ee9ca4d", - "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed" + "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed", + "versions.yml:md5,cb83982d3231b281882f4ddc478d93ae" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-10-07T13:34:18.847540046" + "timestamp": "2024-10-11T10:47:43.954466231" }, "severus, fasta, svdb, vep_cache, '110', vep_plugins": { "content": [ [ "versions.yml:md5,84c59e3a0a183b01a21620b16ee9ca4d", - "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed" + "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed", + "versions.yml:md5,cb83982d3231b281882f4ddc478d93ae" ], "28e9be031273d5e4a94a8654da6e56ed", "test_svs_annotated.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-10-07T13:32:21.970341761" + "timestamp": "2024-10-11T10:47:32.194191605" } } \ No newline at end of file From 6b518cbdd2d01c4405ac74886b3e3f483bdaf949 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Fri, 11 Oct 2024 10:52:31 +0200 Subject: [PATCH 8/8] prettier --- modules.json | 222 +++++++++++++-------------------------------------- 1 file changed, 56 insertions(+), 166 deletions(-) diff --git a/modules.json b/modules.json index eab3a75b..57a6055f 100644 --- a/modules.json +++ b/modules.json @@ -8,370 +8,266 @@ "bcftools/annotate": { "branch": "master", "git_sha": "682f789f93070bd047868300dd018faf3d434e7c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/merge": { "branch": "master", "git_sha": "99a7e61b359f7b7b379cee49259879942d2d2533", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/pluginsplit": { "branch": "master", "git_sha": "c5abf7acbb2943bf09f4025cacbbcc2bc2292637", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/query": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/stats": { "branch": "master", "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/view": { "branch": "master", "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cadd": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "deepvariant": { "branch": "master", "git_sha": "a7e8b8afd4fa82f20d745fa778bfdbf39c1f7efb", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "fastqc": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gawk": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "genmod/annotate": { "branch": "master", "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "genmod/compound": { "branch": "master", "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "genmod/models": { "branch": "master", "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "genmod/score": { "branch": "master", "git_sha": "55692e15e2ef8be6b37ad1475944a338770b4b3e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gfastats": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "glnexus": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hifiasm": { "branch": "master", "git_sha": "aecb06fcdb995ff3e3df7c7a1fd119367d6d1996", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "longphase/haplotag": { "branch": "master", "git_sha": "22fc6d90be8eca2cf6afe5d10b3c5cffcdbcb19c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "longphase/phase": { "branch": "master", "git_sha": "22fc6d90be8eca2cf6afe5d10b3c5cffcdbcb19c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "minimap2/align": { "branch": "master", "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "minimap2/index": { "branch": "master", "git_sha": "72e277acfd9e61a9f1368eafb4a9e83f5bcaa9f5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "modkit/pileup": { "branch": "master", "git_sha": "e29c9dda946de3c4d310d0b3f75664f0f3d5a842", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "paraphase": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/fastq": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/import": { "branch": "master", "git_sha": "90b63cde0f838ca4da3a88a37a5309888cae97b9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "e9bc33485e420b51cfbed3cf63ac7463cd5739d3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "severus": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sniffles": { "branch": "master", "git_sha": "b50aa17b1b604c7b3cfe58a2472d1e7b990ae8bf", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/sniffles/sniffles.diff" }, "somalier/extract": { "branch": "master", "git_sha": "458c882987320e27fc90723ec96c127a243a5497", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/somalier/extract/somalier-extract.diff" }, "somalier/relate": { "branch": "master", "git_sha": "458c882987320e27fc90723ec96c127a243a5497", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "splitubam": { "branch": "master", "git_sha": "d12bb6cdcd22ef8f26803a6a55e918ac017176e8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "stranger": { "branch": "master", "git_sha": "4806239588f35d27a95b187b4000d80e15152022", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/query": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/untar/untar.diff" } } @@ -381,26 +277,20 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +}