From d29582a70a2312918611b4404e3c3c9e03f7579f Mon Sep 17 00:00:00 2001 From: fellen31 Date: Thu, 18 Jul 2024 12:59:01 +0200 Subject: [PATCH] parallel snv-annotation --- CHANGELOG.md | 9 + conf/modules/general.config | 32 +- conf/modules/rank_variants.config | 6 +- conf/modules/short_variant_calling.config | 44 +- conf/modules/snv_annotation.config | 12 - docs/output.md | 15 +- modules.json | 2 +- modules/nf-core/sniffles/main.nf | 3 - modules/nf-core/sniffles/meta.yml | 2 +- modules/nf-core/sniffles/sniffles.diff | 38 +- modules/nf-core/tabix/bgzip/environment.yml | 4 +- nextflow.config | 1 + nextflow_schema.json | 4 + subworkflows/local/rank_variants/main.nf | 5 +- .../local/short_variant_calling/main.nf | 105 ++- .../short_variant_calling/tests/main.nf.test | 24 +- .../tests/main.nf.test.snap | 752 ++++++++++++------ .../tests/nextflow.config | 62 +- .../local/snv_annotation/tests/main.nf.test | 4 +- .../snv_annotation/tests/main.nf.test.snap | 164 ++++ .../snv_annotation/tests/nextflow.config | 79 +- .../local/utils_nfcore_nallo_pipeline/main.nf | 13 + tests/main.nf.test | 44 +- workflows/nallo.nf | 116 ++- 24 files changed, 1002 insertions(+), 538 deletions(-) create mode 100644 subworkflows/local/snv_annotation/tests/main.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index d12c7a6b..26ec5974 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#245](https://github.com/genomic-medicine-sweden/nallo/pull/245) - Added repeat annotation with Stranger - [#252](https://github.com/genomic-medicine-sweden/nallo/pull/252) - Added a new `SCATTER_GENOME` subworkflow - [#255](https://github.com/genomic-medicine-sweden/nallo/pull/255) - Added a new `RANK_VARIANTS` subworkflow to rank SNVs using genmod +- [#261](https://github.com/genomic-medicine-sweden/nallo/pull/261) - Added a `--skip_rank_variants` parameter to skip the rank_variants subworkflow ### `Changed` @@ -35,6 +36,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#251](https://github.com/genomic-medicine-sweden/nallo/pull/251) - Switched from annotating single sample VCFs to annotating a multisample VCF, splitting the VCF per sample afterwards to keep outputs almost consistent - [#256](https://github.com/genomic-medicine-sweden/nallo/pull/256) - Changed Stranger to annotate single-sample VCFs instead of a multi-sample VCF - [#258](https://github.com/genomic-medicine-sweden/nallo/pull/258) - Updated test profile parameters to speed up tests +- [#261](https://github.com/genomic-medicine-sweden/nallo/pull/261) - Changed SNV annotation to run in parallel +- [#261](https://github.com/genomic-medicine-sweden/nallo/pull/261) - Changed SNV output file names and directory structure ### `Removed` @@ -57,6 +60,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | `--extra_gvcfs` | | | `--skip_repeat_wf` | `--skip_repeat_calling` | | `--skip_repeat_wf` | `--skip_repeat_annotation` | +| | `--skip_rank_variants` | + +> [!NOTE] +> Parameter has been updated if both old and new parameter information is present. +> Parameter has been added if just the new parameter information is present. +> Parameter has been removed if new parameter information isn't present. ## v0.2.0 - [2024-06-26] diff --git a/conf/modules/general.config b/conf/modules/general.config index 3b944088..3a6c233b 100644 --- a/conf/modules/general.config +++ b/conf/modules/general.config @@ -24,16 +24,40 @@ process { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ + withName: '.*:NALLO:BCFTOOLS_CONCAT' { + ext.prefix = { params.skip_snv_annotation ? "${meta.id}_snv" : "${meta.id}_snv_annotated" } + ext.args = { [ + '--allow-overlaps', + '--output-type z', + '--write-index=tbi' + ].join(' ') } + publishDir = [ + path: { "${params.outdir}/snvs/multi_sample/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : (!params.skip_rank_variants && !params.skip_snv_annotation ? null : filename) } + ] + } + withName: '.*:NALLO:BCFTOOLS_PLUGINSPLIT' { - ext.prefix = { "${meta.id}_vep" } ext.args = [ '--output-type z', '--write-index=tbi' ].join(' ') publishDir = [ - path: { "${params.outdir}/snv_annotation/vep/single_sample/" }, + path: { "${params.outdir}/snvs/single_sample/" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + // Can't use prefix as it would come from the original file + saveAs: { filename -> + if (filename.equals('versions.yml')) { + null + } else { + def matcher = filename =~ /(.+)(\.vcf\.gz(?:\.tbi)?)$/ + def sample = matcher[0][1] + def extension = matcher[0][2] + def annotated = params.skip_snv_annotation ? "" : (params.skip_rank_variants ? "_annotated" : "_annotated_ranked" ) + "${sample}/${sample}_snv${annotated}${extension}" + } + } ] } withName: '.*:NALLO:FASTQC' { @@ -114,7 +138,7 @@ process { withName: '.*:NALLO:ECHTVAR_ENCODE' { publishDir = [ - path: { "${params.outdir}/snv_annotation/echtvar/encode/${meta.id}" }, + path: { "${params.outdir}/databases/echtvar/encode/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/conf/modules/rank_variants.config b/conf/modules/rank_variants.config index 379eb62f..db473932 100644 --- a/conf/modules/rank_variants.config +++ b/conf/modules/rank_variants.config @@ -46,9 +46,9 @@ process { } withName: '.*:RANK_VARIANTS_SNV:TABIX_BGZIP' { - ext.prefix = { "${meta.id}_snv_ranked" } + ext.prefix = { "${meta.id}_snv_annotated_ranked" } publishDir = [ - path: { "${params.outdir}/ranked_variants" }, + path: { "${params.outdir}/snvs/multi_sample/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -56,7 +56,7 @@ process { withName: '.*:RANK_VARIANTS_SNV:TABIX_TABIX' { publishDir = [ - path: { "${params.outdir}/ranked_variants" }, + path: { "${params.outdir}/snvs/multi_sample/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/conf/modules/short_variant_calling.config b/conf/modules/short_variant_calling.config index 1f0893e1..18a49b49 100644 --- a/conf/modules/short_variant_calling.config +++ b/conf/modules/short_variant_calling.config @@ -37,56 +37,30 @@ process { ext.args = '--config DeepVariant_unfiltered' } - withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_CONCAT_GVCF' { + withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_CONCAT' { ext.args = '--allow-overlaps' } - withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_CONCAT_VCF' { - ext.args = '--allow-overlaps' - } - - withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_SORT_GVCF' { - ext.prefix = { "${vcf.simpleName}_sorted.g" } - ext.args = [ - '--output-type z', - '--write-index=tbi' - ].join(' ') - publishDir = [ - path: { "${params.outdir}/snv_calling/single_sample/deepvariant/gvcf/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_SORT_VCF' { - ext.prefix = { "${vcf.simpleName}_sorted" } + withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_NORM_SINGLESAMPLE' { + ext.prefix = { "${meta.id}_deepvariant_snv" } ext.args = [ - '--output-type z', - '--write-index=tbi' + '-m -', + '-w 10000', + '--output-type u', ].join(' ') - publishDir = [ - path: { "${params.outdir}/snv_calling/single_sample/deepvariant/vcf/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_FILLTAGS' { ext.prefix = { "${meta.id}_ac" } - ext.args = '--output-type b' + ext.args = '--output-type u' } - withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_NORM' { + withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_NORM_MULTISAMPLE' { ext.args = [ '-m -', - '--output-type b', + '--output-type u', '--write-index=csi', '-w 10000' ].join(' ') - publishDir = [ - path: { "${params.outdir}/snv_calling/multi_sample/glnexus/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml')? null : (meta.id == "multisample" ? filename : null)} - ] } } diff --git a/conf/modules/snv_annotation.config b/conf/modules/snv_annotation.config index 6bf3ceeb..a0695112 100644 --- a/conf/modules/snv_annotation.config +++ b/conf/modules/snv_annotation.config @@ -45,18 +45,6 @@ process { '--uniprot --vcf', '--no_stats' ].join(' ') } - publishDir = [ - path: { "${params.outdir}/snv_annotation/vep/multi_sample/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } - withName: '.*:SNV_ANNOTATION:TABIX_VEP' { - publishDir = [ - path: { "${params.outdir}/snv_annotation/vep/multi_sample/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } } diff --git a/docs/output.md b/docs/output.md index 013a9eba..edb68d87 100644 --- a/docs/output.md +++ b/docs/output.md @@ -301,11 +301,11 @@ In case of affected samples, [echtvar](https://github.com/brentp/echtvar) and [V
Output files from SNV Annotation -- `{outputdir}/snv_annotation/echtvar/encode/multisample/` +- `{outputdir}/databases/echtvar/encode/multisample/` - `*.zip`: Database with AF and AC for all samples run -- `{outputdir}/snv_annotation/vep/{single_sample,multi_sample/multisample}/` - - `*.vcf.gz`: VCF with annotated variants - - `*.vcf.gz.tbi`: Index of the corresponding VCF file +- `{outputdir}/snvs/{single_sample,multi_sample/multisample}/` + - `*_snvs_annotated*.vcf.gz`: VCF with annotated variants + - `*_snvs_annotated*.vcf.gz.tbi`: Index of the corresponding VCF file
### Ranked variants @@ -321,9 +321,10 @@ In case of affected samples, [echtvar](https://github.com/brentp/echtvar) and [V
Output files -- `{outputdir}ranked_variants/` - - `*_snv_ranked.vcf.gz`: file containing SNV annotations with their rank scores (does not include mitochondrial variants). - - `*_snv_ranked.vcf.gz.tbi`: index of the file containing SNV annotations with their rank scores. +- `{outputdir}/snvs/{single_sample,multi_sample/multisample}/` + - `*_snvs_annotated_ranked.vcf.gz`: VCF with annotated and ranked variants + - `*_snvs_annotated_ranked.vcf.gz.tbi`: Index of the corresponding VCF file +
### SNV Calling diff --git a/modules.json b/modules.json index 88cb96db..05e1e0e5 100644 --- a/modules.json +++ b/modules.json @@ -190,7 +190,7 @@ }, "sniffles": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "b50aa17b1b604c7b3cfe58a2472d1e7b990ae8bf", "installed_by": ["modules"], "patch": "modules/nf-core/sniffles/sniffles.diff" }, diff --git a/modules/nf-core/sniffles/main.nf b/modules/nf-core/sniffles/main.nf index 83f63586..41bc76c1 100644 --- a/modules/nf-core/sniffles/main.nf +++ b/modules/nf-core/sniffles/main.nf @@ -49,7 +49,6 @@ process SNIFFLES { stub: def prefix = task.ext.prefix ?: "${meta.id}" - """ touch ${prefix}.vcf.gz touch ${prefix}.snf @@ -59,6 +58,4 @@ process SNIFFLES { sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //') END_VERSIONS """ - } - diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml index 333d5de1..c8b2da7d 100644 --- a/modules/nf-core/sniffles/meta.yml +++ b/modules/nf-core/sniffles/meta.yml @@ -3,7 +3,7 @@ description: structural-variant calling with sniffles keywords: - sniffles - structural-variant calling - - long-read sequencing + - long-read tools: - sniffles: description: a fast structural variant caller for long-read sequencing diff --git a/modules/nf-core/sniffles/sniffles.diff b/modules/nf-core/sniffles/sniffles.diff index 9b8461a9..9b748dd3 100644 --- a/modules/nf-core/sniffles/sniffles.diff +++ b/modules/nf-core/sniffles/sniffles.diff @@ -1,15 +1,7 @@ Changes in module 'nf-core/sniffles' --- modules/nf-core/sniffles/meta.yml +++ modules/nf-core/sniffles/meta.yml -@@ -3,6 +3,7 @@ - keywords: - - sniffles - - structural-variant calling -+ - long-read sequencing - tools: - - sniffles: - description: a fast structural variant caller for long-read sequencing -@@ -16,10 +17,10 @@ +@@ -17,10 +17,10 @@ description: | Groovy Map containing sample information e.g. [ id:'test' ] @@ -23,7 +15,7 @@ Changes in module 'nf-core/sniffles' - bai: type: file description: Index of BAM file -@@ -33,6 +34,15 @@ +@@ -34,6 +34,15 @@ type: file description: | Reference database in FASTA format @@ -39,7 +31,7 @@ Changes in module 'nf-core/sniffles' output: - meta: type: map -@@ -45,8 +55,8 @@ +@@ -46,8 +55,8 @@ pattern: "*.vcf.gz" - snf: type: file @@ -76,7 +68,7 @@ Changes in module 'nf-core/sniffles' when: task.ext.when == null || task.ext.when -@@ -23,18 +26,39 @@ +@@ -23,14 +26,33 @@ script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" @@ -99,26 +91,20 @@ Changes in module 'nf-core/sniffles' + $snf \\ $args + - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //') - END_VERSIONS - """ ++ cat <<-END_VERSIONS > versions.yml ++ "${task.process}": ++ sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //') ++ END_VERSIONS ++ """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" -+ + """ + touch ${prefix}.vcf.gz + touch ${prefix}.snf + -+ cat <<-END_VERSIONS > versions.yml -+ "${task.process}": -+ sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //') -+ END_VERSIONS -+ """ -+ - } - + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //') ************************************************************ diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 361c078b..0fe9c023 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,8 +1,10 @@ name: tabix_bgzip + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.19.1 + - bioconda::tabix=1.11 diff --git a/nextflow.config b/nextflow.config index 5f30e8dd..5bbd55b5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -33,6 +33,7 @@ params { skip_assembly_wf = params.preset == 'ONT_R10' ? true : false skip_mapping_wf = false skip_methylation_wf = params.preset == 'pacbio' ? true : false + skip_rank_variants = false skip_repeat_calling = params.preset == 'ONT_R10' ? true : false skip_repeat_annotation = params.preset == 'ONT_R10' ? true : false skip_phasing_wf = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 8f3ae975..cd4df12e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -62,6 +62,10 @@ "skip_call_paralogs": { "type": "boolean", "description": "Skip call paralogs (Paraphase)" + }, + "skip_rank_variants": { + "type": "boolean", + "description": "Skip rank variants workflow" } }, "fa_icon": "fas fa-american-sign-language-interpreting" diff --git a/subworkflows/local/rank_variants/main.nf b/subworkflows/local/rank_variants/main.nf index c2229ee8..c6820e14 100644 --- a/subworkflows/local/rank_variants/main.nf +++ b/subworkflows/local/rank_variants/main.nf @@ -46,6 +46,7 @@ workflow RANK_VARIANTS { ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) emit: - vcf = ch_vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] + tbi = TABIX_TABIX.out.tbi // channel: [ val(meta), path(tbi) ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/short_variant_calling/main.nf b/subworkflows/local/short_variant_calling/main.nf index 8bdaf9f5..c769a3fd 100644 --- a/subworkflows/local/short_variant_calling/main.nf +++ b/subworkflows/local/short_variant_calling/main.nf @@ -1,11 +1,12 @@ -include { DEEPVARIANT } from '../../../modules/nf-core/deepvariant' -include { GLNEXUS } from '../../../modules/nf-core/glnexus' -include { BCFTOOLS_CONCAT as BCFTOOLS_CONCAT_GVCF } from '../../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_CONCAT as BCFTOOLS_CONCAT_VCF } from '../../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_FILLTAGS } from '../../../modules/local/bcftools/filltags/main' -include { BCFTOOLS_NORM } from '../../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_SORT as BCFTOOLS_SORT_GVCF } from '../../../modules/nf-core/bcftools/sort/main' -include { BCFTOOLS_SORT as BCFTOOLS_SORT_VCF } from '../../../modules/nf-core/bcftools/sort/main' +// +// Workflow to call and merge SNVs +// +include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_FILLTAGS } from '../../../modules/local/bcftools/filltags/main' +include { BCFTOOLS_NORM as BCFTOOLS_NORM_MULTISAMPLE } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as BCFTOOLS_NORM_SINGLESAMPLE } from '../../../modules/nf-core/bcftools/norm/main' +include { DEEPVARIANT } from '../../../modules/nf-core/deepvariant' +include { GLNEXUS } from '../../../modules/nf-core/glnexus' workflow SHORT_VARIANT_CALLING { @@ -18,58 +19,54 @@ workflow SHORT_VARIANT_CALLING { main: ch_versions = Channel.empty() - DEEPVARIANT ( ch_bam_bai_bed, ch_fasta, ch_fai, [[],[]] ) - ch_versions = ch_versions.mix(DEEPVARIANT.out.versions) - - // gVCF - DEEPVARIANT.out.gvcf - .map { meta, vcf -> [ groupKey(meta, meta.num_intervals ), vcf ] } - .groupTuple() - .join( DEEPVARIANT.out.gvcf_tbi - .map { meta, vcf -> [ groupKey(meta, meta.num_intervals ), vcf ] } - .groupTuple() - ) - .map { meta, vcf, tbi -> - [ meta - meta.subMap('num_intervals'), vcf, tbi ] + ch_bam_bai_bed + // Add call region to meta so we can group by it later + .map { meta, bam, bai, bed -> + [ meta + [ 'region': bed ], bam, bai, bed ] } - .set{ bcftools_concat_gvcf_in } + .set { ch_deepvariant_in } - // Concat into one gVCF per sample & sort - BCFTOOLS_CONCAT_GVCF ( bcftools_concat_gvcf_in ) - ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_GVCF.out.versions) - - BCFTOOLS_SORT_GVCF ( BCFTOOLS_CONCAT_GVCF.out.vcf ) - ch_versions = ch_versions.mix(BCFTOOLS_SORT_GVCF.out.versions) + DEEPVARIANT ( ch_deepvariant_in, ch_fasta, ch_fai, [[],[]] ) + ch_versions = ch_versions.mix(DEEPVARIANT.out.versions) - // VCF + // First remove region so we can group per sample + // Then after grouping remove num_intervals since to match the meta of other workflows DEEPVARIANT.out.vcf - .map { meta, vcf -> [ groupKey(meta, meta.num_intervals ), vcf ] } + .map { meta, vcf -> + new_meta = meta - meta.subMap('region') + [ groupKey(new_meta, new_meta.num_intervals ), vcf ] + } .groupTuple() .join( DEEPVARIANT.out.vcf_tbi - .map { meta, vcf -> [ groupKey(meta, meta.num_intervals ), vcf ] } + .map{ meta, tbi -> + new_meta = meta - meta.subMap('region') + [ groupKey(new_meta, new_meta.num_intervals ), tbi ] + } .groupTuple() ) .map { meta, vcf, tbi -> [ meta - meta.subMap('num_intervals'), vcf, tbi ] } - .set{ bcftools_concat_vcf_in } + .set{ ch_concat_singlesample_in } - // Concat into one VCF per sample & sort - BCFTOOLS_CONCAT_VCF ( bcftools_concat_vcf_in ) - ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_VCF.out.versions) + // This creates a singlesample VCF containing ALL regions + BCFTOOLS_CONCAT ( ch_concat_singlesample_in ) + ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions) - BCFTOOLS_SORT_VCF ( BCFTOOLS_CONCAT_VCF.out.vcf ) - ch_versions = ch_versions.mix(BCFTOOLS_SORT_VCF.out.versions) + // Which is then normalized, and ready to be used + // in processes that require SNVs, but not annotated SNVs + BCFTOOLS_NORM_SINGLESAMPLE ( BCFTOOLS_CONCAT.out.vcf.map { meta, vcf -> [ meta, vcf, [] ] }, ch_fasta ) + ch_versions = ch_versions.mix(BCFTOOLS_NORM_SINGLESAMPLE.out.versions) - // Multisample - BCFTOOLS_SORT_GVCF.out.vcf - .map { meta, gvcf -> [ 'multisample', meta.phenotype == 2, gvcf ] } - .groupTuple() // Group all files together + // This creates a multisample VCF, with regions from ONE bed file + DEEPVARIANT.out.gvcf + .map { meta, gvcf -> [ meta.region.name, meta.phenotype == 2, gvcf ] } + .groupTuple() // Group all files together per region // If any of the samples in the VCF have an affected phenotype (2) // add this to the meta of the multisample VCF to know if we should run RANK_VARIANTS or not - .map { id, affected, gvcfs -> + .map { region, affected, gvcfs -> new_meta = [ - 'id': id, + 'id': region, 'contains_affected': affected.any(), ] [ new_meta, gvcfs ] @@ -83,25 +80,17 @@ workflow SHORT_VARIANT_CALLING { BCFTOOLS_FILLTAGS ( GLNEXUS.out.bcf ) ch_versions = ch_versions.mix(BCFTOOLS_FILLTAGS.out.versions) - // Decompose and normalize variants BCFTOOLS_FILLTAGS.out.vcf - .concat( BCFTOOLS_SORT_VCF.out.vcf) .map { meta, vcf -> [ meta, vcf, [] ] } .set { bcftools_norm_in } - BCFTOOLS_NORM ( bcftools_norm_in, ch_fasta ) - ch_versions = ch_versions.mix(BCFTOOLS_NORM.out.versions) - - // Temporary solution while this workflow still outputs two types of vcfs - BCFTOOLS_NORM.out.vcf - .branch { meta, vcf -> - multisample: meta.id == "multisample" - singlesample: meta.id != "multisample" - } - .set { vcf_out } + // Decompose and normalize variants + BCFTOOLS_NORM_MULTISAMPLE ( bcftools_norm_in, ch_fasta ) + ch_versions = ch_versions.mix(BCFTOOLS_NORM_MULTISAMPLE.out.versions) emit: - snp_calls_vcf = vcf_out.singlesample // channel: [ val(meta), path(vcf) ] - combined_bcf = vcf_out.multisample // channel: [ val(meta), path(bcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] + snp_calls_vcf = BCFTOOLS_NORM_SINGLESAMPLE.out.vcf // channel: [ val(meta), path(bcf) ] + combined_bcf = BCFTOOLS_NORM_MULTISAMPLE.out.vcf // channel: [ val(meta), path(bcf) ] + combined_csi = BCFTOOLS_NORM_MULTISAMPLE.out.csi // channel: [ val(meta), path(csi) ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test b/subworkflows/local/short_variant_calling/tests/main.nf.test index ee10b73b..b26175a9 100644 --- a/subworkflows/local/short_variant_calling/tests/main.nf.test +++ b/subworkflows/local/short_variant_calling/tests/main.nf.test @@ -10,12 +10,12 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false, num_intervals:1 ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] - ] + ]) input[1] = [ [ id:'genome'], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -43,12 +43,12 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false, num_intervals:1 ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) - ] + ]) input[1] = [ [ id:'genome'], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -77,12 +77,12 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false, num_intervals:1 ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) - ] + ]) input[1] = [ [ id:'genome'], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -218,12 +218,12 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false, num_intervals:1 ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] - ] + ]) input[1] = [ [ id:'genome'], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -254,12 +254,12 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false, num_intervals:1 ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) - ] + ]) input[1] = [ [ id:'genome'], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) @@ -290,12 +290,12 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false, num_intervals:1 ], // meta map file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) - ] + ]) input[1] = [ [ id:'genome'], file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap index e0400854..6d3ce14a 100644 --- a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap +++ b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap @@ -8,36 +8,51 @@ "id": "test", "single_end": false }, - "test_concat_vcf.vcf.gz_sorted.vcf.gz_norm.vcf.gz:md5,d8a35574801cfec345629770bfae2de7" + "test_norm_singlesample.bcf:md5,41728ff8745b959f29f7c63b262b36a8" ] ], "1": [ [ { - "id": "multisample", + "id": "genome.bed", "contains_affected": false }, - "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" + "genome.bed_norm_multisample.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" ] ], "2": [ + [ + { + "id": "genome.bed", + "contains_affected": false + }, + "genome.bed_norm_multisample.vcf.gz.csi:md5,53e24fb59fef3bee6291c474e20200b9" + ] + ], + "3": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,24d51016afc8125a2ef4f5ba42a07bab", - "versions.yml:md5,24d51016afc8125a2ef4f5ba42a07bab", "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6", - "versions.yml:md5,69acb554aff0d931eda1843a5aaa0b89", - "versions.yml:md5,cb16914849e7996a54a7125e36c96576", - "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", - "versions.yml:md5,f0fdcc8697bb029a433cc4ba12f3c105", - "versions.yml:md5,f41077fceba2b7405542dfe054f2225a" + "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", + "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", + "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", + "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6" ], "combined_bcf": [ [ { - "id": "multisample", + "id": "genome.bed", "contains_affected": false }, - "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" + "genome.bed_norm_multisample.vcf.gz:md5,e6dd7f56772c154750e937d9a56baa6d" + ] + ], + "combined_csi": [ + [ + { + "id": "genome.bed", + "contains_affected": false + }, + "genome.bed_norm_multisample.vcf.gz.csi:md5,53e24fb59fef3bee6291c474e20200b9" ] ], "snp_calls_vcf": [ @@ -46,27 +61,24 @@ "id": "test", "single_end": false }, - "test_concat_vcf.vcf.gz_sorted.vcf.gz_norm.vcf.gz:md5,d8a35574801cfec345629770bfae2de7" + "test_norm_singlesample.bcf:md5,41728ff8745b959f29f7c63b262b36a8" ] ], "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - 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"test2_concat_vcf.vcf.gz_sorted.vcf.gz_norm.vcf.gz:md5,0ce965213b3c4fa10f5e855e0254cc0e" + "test2_norm_singlesample.bcf:md5,6d3448d142f8a0d11ced3b57322fc39c" ] ], "1": [ [ { - "id": "multisample", + "id": "genome.bed", "contains_affected": false }, - "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,7533ee89ae115f8f78ac26d29efc78d3" + "genome.bed_norm_multisample.vcf.gz:md5,7533ee89ae115f8f78ac26d29efc78d3" + ], + [ + { + "id": "genome.blacklist_intervals.bed", + "contains_affected": false + }, + "genome.blacklist_intervals.bed_norm_multisample.vcf.gz:md5,e01b4f349dbb9a7da597262fac9c7675" ] ], "2": [ + [ + { + "id": "genome.bed", + "contains_affected": false + }, + "genome.bed_norm_multisample.vcf.gz.csi:md5,74d344e326afc8af7bbc7c8799d4b5e2" + ], + [ + { + "id": "genome.blacklist_intervals.bed", + "contains_affected": false + }, + "genome.blacklist_intervals.bed_norm_multisample.vcf.gz.csi:md5,bed9fa291c220a1ba04eb2d448932ffc" + ] + ], + "3": [ + "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - 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"versions.yml:md5,f0fdcc8697bb029a433cc4ba12f3c105", - "versions.yml:md5,f41077fceba2b7405542dfe054f2225a", - "versions.yml:md5,f41077fceba2b7405542dfe054f2225a" + "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6" ], "combined_bcf": [ [ { - "id": "multisample", + "id": "genome.bed", + "contains_affected": false + }, + "genome.bed_norm_multisample.vcf.gz:md5,7533ee89ae115f8f78ac26d29efc78d3" + ], + [ + { + "id": "genome.blacklist_intervals.bed", "contains_affected": false }, - "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,7533ee89ae115f8f78ac26d29efc78d3" + "genome.blacklist_intervals.bed_norm_multisample.vcf.gz:md5,e01b4f349dbb9a7da597262fac9c7675" + ] + ], + "combined_csi": [ + [ + { + "id": "genome.bed", + "contains_affected": false + }, + "genome.bed_norm_multisample.vcf.gz.csi:md5,74d344e326afc8af7bbc7c8799d4b5e2" + ], + [ + { + "id": "genome.blacklist_intervals.bed", + "contains_affected": false + }, + "genome.blacklist_intervals.bed_norm_multisample.vcf.gz.csi:md5,bed9fa291c220a1ba04eb2d448932ffc" ] ], "snp_calls_vcf": [ @@ -130,42 +185,39 @@ "id": "test", "single_end": false }, - 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"versions.yml:md5,24d51016afc8125a2ef4f5ba42a07bab", - "versions.yml:md5,24d51016afc8125a2ef4f5ba42a07bab", "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6", "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6", - "versions.yml:md5,69acb554aff0d931eda1843a5aaa0b89", - "versions.yml:md5,cb16914849e7996a54a7125e36c96576", + "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", + "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", + "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", + "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", - "versions.yml:md5,f0fdcc8697bb029a433cc4ba12f3c105", - "versions.yml:md5,f41077fceba2b7405542dfe054f2225a" + "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6" ], "combined_bcf": [ [ { - "id": "multisample", + "id": "genome.bed", "contains_affected": false }, - "multisample.bcf_filltags.vcf_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "genome.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ], + [ + { + "id": "genome.blacklist_intervals.bed", + "contains_affected": false + }, + "genome.blacklist_intervals.bed_norm_multisample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "combined_csi": [ + [ + { + "id": "genome.bed", + "contains_affected": false + }, + "genome.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "genome.blacklist_intervals.bed", + "contains_affected": false + }, + "genome.blacklist_intervals.bed_norm_multisample.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "snp_calls_vcf": [ @@ -730,27 +990,27 @@ "id": "test", "single_end": false }, - "test_concat_vcf.vcf.gz_sorted.vcf.gz_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_norm_singlesample.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,24d51016afc8125a2ef4f5ba42a07bab", - "versions.yml:md5,24d51016afc8125a2ef4f5ba42a07bab", + "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6", "versions.yml:md5,38fcec4389d89d9ebbdaa63f369600f6", - "versions.yml:md5,69acb554aff0d931eda1843a5aaa0b89", - "versions.yml:md5,cb16914849e7996a54a7125e36c96576", + "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", + "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", + "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", + "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", - "versions.yml:md5,f0fdcc8697bb029a433cc4ba12f3c105", - "versions.yml:md5,f41077fceba2b7405542dfe054f2225a" + "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-07-17T15:33:18.116317115" + "timestamp": "2024-07-22T16:25:27.04221622" } } \ No newline at end of file diff --git a/subworkflows/local/short_variant_calling/tests/nextflow.config b/subworkflows/local/short_variant_calling/tests/nextflow.config index e05a3b72..f9b1d1a5 100644 --- a/subworkflows/local/short_variant_calling/tests/nextflow.config +++ b/subworkflows/local/short_variant_calling/tests/nextflow.config @@ -3,32 +3,50 @@ process { ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" } ext.args = { [ '--model_type WGS', - "--sample_name=${meta.id}" - ].join(' ') } + "--sample_name=${meta.id}", + '-vcf_stats_report=False' + ].join(' ') } } + withName: 'GLNEXUS' { ext.args = '--config DeepVariant_unfiltered' } - withName: 'BCFTOOLS_CONCAT_GVCF' { - ext.prefix = { "${meta.id}_concat_gvcf" } - ext.args = '--no-version' - } - withName: 'BCFTOOLS_CONCAT_VCF' { - ext.prefix = { "${meta.id}_concat_vcf" } - ext.args = '--no-version' - } - withName: 'BCFTOOLS_SORT_GVCF' { - ext.prefix = { "${vcf}_sorted.g" } - } - withName: 'BCFTOOLS_SORT_VCF' { - ext.prefix = { "${vcf}_sorted" } - } + + withName: 'BCFTOOLS_CONCAT' { + ext.prefix = { "${meta.id}_concat" } + ext.args = [ + '--no-version', + '--allow-overlaps' + ].join(' ') + } + + withName: 'BCFTOOLS_NORM_MULTISAMPLE' { + ext.prefix = { "${meta.id}_norm_multisample" } + ext.args = [ + '--no-version', + '-m -', + '--output-type z', + '--write-index=csi', + '-w 10000' + ].join(' ') + } + + withName: 'BCFTOOLS_NORM_SINGLESAMPLE' { + ext.prefix = { "${meta.id}_norm_singlesample" } + ext.args = [ + '--no-version', + '-m -', + '-w 10000', + '--output-type u', + ].join(' ') + } + withName: 'BCFTOOLS_FILLTAGS' { - ext.prefix = { "${vcf}_filltags" } - ext.args = '--no-version' - } - withName: 'BCFTOOLS_NORM' { - ext.prefix = { "${vcf}_norm" } - ext.args = '--no-version' + ext.prefix = { "${meta.id}_ac" } + ext.args = [ + '--no-version', + '--output-type u' + ].join(' ') } + } diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test b/subworkflows/local/snv_annotation/tests/main.nf.test index 224a24f0..ac3de6b3 100644 --- a/subworkflows/local/snv_annotation/tests/main.nf.test +++ b/subworkflows/local/snv_annotation/tests/main.nf.test @@ -78,8 +78,6 @@ nextflow_workflow { test("bcf, db, vep_cache, '110'") { when { - params { - } workflow { """ input[0] = SHORT_VARIANT_CALLING.out.combined_bcf @@ -99,7 +97,7 @@ nextflow_workflow { { assert snapshot( workflow.out.versions, file(workflow.out.tbi.get(0).get(1)).name, - path(workflow.out.vcf.get(0).get(1)).linesGzip[45..118], // Stable + path(workflow.out.vcf.get(0).get(1)).linesGzip[47..118], // Stable path(workflow.out.vcf.get(0).get(1)).linesGzip[120..156] // Stable ).match() } ) diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test.snap b/subworkflows/local/snv_annotation/tests/main.nf.test.snap new file mode 100644 index 00000000..a1a7725e --- /dev/null +++ b/subworkflows/local/snv_annotation/tests/main.nf.test.snap @@ -0,0 +1,164 @@ +{ + "bcf, db, vep_cache, '110', -stub": { + "content": [ + [ + "versions.yml:md5,275497de0e23f331b5b5eeb47799c8e9", + "versions.yml:md5,797275193dd19766e99030e63c23bd5f", + "versions.yml:md5,a07924ee4ebc2d4de5bb7ef897ddc30c", + "versions.yml:md5,c0e55e36a31ed71acf25702b7d059533" + ], + [ + [ + { + "id": "test_data.bed", + "contains_affected": false + }, + "test_data.bed.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "test_data.bed", + "contains_affected": false + }, + "test_data.bed.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T15:53:41.338180873" + }, + "bcf, db, vep_cache, '110'": { + "content": [ + [ + "versions.yml:md5,797275193dd19766e99030e63c23bd5f", + "versions.yml:md5,89437847140da33e3bfb17867507f30d", + "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\t12\t.\tAF=1;AQ=12;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\t1/1:13:0,13:5:12,4,0:..", + "chr16\t86889\tchr16_86889_T_C\tT\tC\t18\t.\tAF=1;AQ=18;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\t1/1:28:0,28:16:18,19,0:..", + "chr16\t160055\tchr16_160055_C_G\tC\tG\t10\t.\tAF=1;AQ=10;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\t1/1:30:0,29:11:10,22,0:..", + "chr16\t160180\tchr16_160180_C_T\tC\tT\t13\t.\tAF=1;AQ=13;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\t1/1:29:1,28:12:13,15,0:..", + "chr16\t160216\tchr16_160216_T_A\tT\tA\t2\t.\tAF=0.5;AQ=2;AC=1;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\t0/1:30:0,27:2:2,0,5:..", + "chr16\t160217\tchr16_160217_C_T\tC\tT\t1\t.\tAF=0.5;AQ=1;AC=1;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\t./1:27:.,27:.:0,0,0:O.", + "chr16\t160326\tchr16_160326_T_A\tT\tA\t12\t.\tAF=1;AQ=12;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\t1/1:30:0,29:11:12,16,0:..", + "chr16\t160327\tchr16_160327_C_T\tC\tT\t11\t.\tAF=1;AQ=11;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\t1/1:29:3,26:11:11,18,0:..", + "chr16\t160388\tchr16_160388_G_GGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\tG\tGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCCGGGATGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCTGGGATGGCTTGTGGGGCACAGGTTGTGAGAGGTGCCTGGGACGGCTTGTGGGGCACAGGTTGTGAGA\t7\t.\tAF=0.5;AQ=7;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\t0/1:31:4,14:5:7,0,4:..", + "chr16\t160718\tchr16_160718_A_ATGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGG\tA\tATGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGG\t4\t.\tAF=0.5;AQ=4;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=TGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGG|upstream_gene_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene|||||||||||2403|1||HGNC|HGNC:4836,TGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGG|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,TGCCCGGGATGGCTTGTGGGGCACAGGTTGTGAGGGGTGCCCGGGACGGCTTGTGGGGCACAGGCTGTGAGGGTGCCCAGGATGGCTTGTGGGGCACAGGCTGCAAGAGGTGCCCAGGACGGCTTGTGGGGCACAGGTTGTGAGGG|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000496585|protein_coding_CDS_not_defined|||||||||||3763|1||HGNC|HGNC:4826\tGT:DP:AD:GQ:PL:RNC\t0/1:30:22,4:6:4,0,22:..", + "chr16\t160728\tchr16_160728_C_T\tC\tT\t2\t.\tAF=0.5;AQ=2;AC=1;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\t0/1:30:8,22:4:2,0,7:..", + "chr16\t160746\tchr16_160746_T_C\tT\tC\t3\t.\tAF=0.5;AQ=3;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\t0/1:30:23,7:5:3,0,18:..", + "chr16\t161474\tchr16_161474_TA_T\tTA\tT\t4\t.\tAF=0.5;AQ=4;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\t0/1:25:16,9:6:4,0,29:..", + "chr16\t162329\tchr16_162329_G_A\tG\tA\t16\t.\tAF=0.5;AQ=16;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\t0/1:23:15,8:17:16,0,36:..", + "chr16\t162650\tchr16_162650_C_T\tC\tT\t17\t.\tAF=0.5;AQ=17;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\t0/1:24:9,15:17:17,0,30:..", + "chr16\t163106\tchr16_163106_C_T\tC\tT\t13\t.\tAF=0.5;AQ=13;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\t0/1:23:15,8:13:13,0,35:..", + "chr16\t163140\tchr16_163140_T_G\tT\tG\t8\t.\tAF=0.5;AQ=8;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\t0/1:23:15,8:9:8,0,33:..", + "chr16\t163143\tchr16_163143_G_A\tG\tA\t1\t.\tAF=0.5;AQ=1;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\t0/1:23:15,8:4:1,0,27:..", + "chr16\t163796\tchr16_163796_T_A\tT\tA\t10\t.\tAF=1;AQ=10;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\t1/1:15:0,15:8:10,9,0:..", + "chr16\t163800\tchr16_163800_G_A\tG\tA\t13\t.\tAF=1;AQ=13;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\t1/1:16:2,14:8:13,9,0:..", + "chr16\t163804\tchr16_163804_G_A\tG\tA\t16\t.\tAF=1;AQ=16;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\t1/1:21:0,21:14:16,18,0:..", + "chr16\t164431\tchr16_164431_T_TG\tT\tTG\t21\t.\tAF=1;AQ=21;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\t1/1:21:0,21:17:21,18,0:..", + "chr16\t164541\tchr16_164541_G_GGTCC\tG\tGGTCC\t23\t.\tAF=0.5;AQ=23;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\t0/1:21:13,7:23:23,0,39:..", + "chr16\t164690\tchr16_164690_C_CGCGGGGCGCGGTGCGGGCGGG\tC\tCGCGGGGCGCGGTGCGGGCGGG\t20\t.\tAF=0.5;AQ=20;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\t0/1:21:6,14:19:20,0,22:..", + "chr16\t164723\tchr16_164723_C_T\tC\tT\t12\t.\tAF=0.5;AQ=12;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\t0/1:21:15,4:13:12,0,30:..", + "chr16\t164731\tchr16_164731_C_CG;chr16_164731_C_CGGGGTCGCG\tC\tCG\t11\t.\tAF=0.5;AQ=11;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\t1/0:21:2,14:9:19,11,18:..", + "chr16\t164731\tchr16_164731_C_CG;chr16_164731_C_CGGGGTCGCG\tC\tCGGGGTCGCG\t11\t.\tAF=0.5;AQ=11;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=GGGGTCGCG|intron_variant&non_coding_transcript_variant|MODIFIER|HBZP1|ENSG00000206178|Transcript|ENST00000354915|unprocessed_pseudogene||2/2||||||||||1||HGNC|HGNC:4836,GGGGTCGCG|upstream_gene_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000356815|protein_coding|||||||||||1246|1||HGNC|HGNC:4826,GGGGTCGCG|upstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3947|1||HGNC|HGNC:4825,GGGGTCGCG|intron_variant&non_coding_transcript_variant|MODIFIER|HBM|ENSG00000206177|Transcript|ENST00000472539|protein_coding_CDS_not_defined||1/2||||||||||1||HGNC|HGNC:4826,GGGGTCGCG|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\t0/1:21:2,4:9:19,11,34:..", + "chr16\t164740\tchr16_164740_C_T\tC\tT\t8\t.\tAF=1;AQ=8;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|||||||||||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\t1/1:20:1,18:7:8,9,0:..", + "chr16\t164771\tchr16_164771_T_C\tT\tC\t19\t.\tAF=0.5;AQ=19;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\t0/1:21:13,6:20:19,0,34:..", + "chr16\t164791\tchr16_164791_G_A\tG\tA\t25\t.\tAF=0.5;AQ=25;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\t0/1:21:6,15:20:25,0,20:..", + "chr16\t164800\tchr16_164800_G_GGCGGGGTCGCGGGGCGGGGCGAGGTC\tG\tGGCGGGGTCGCGGGGCGGGGCGAGGTC\t3\t.\tAF=0.5;AQ=3;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\t0/1:21:14,4:5:3,0,24:..", + "chr16\t164817\tchr16_164817_C_A\tC\tA\t27\t.\tAF=0.5;AQ=27;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\t0/1:21:8,13:24:27,0,26:..", + "chr16\t164831\tchr16_164831_C_CG\tC\tCG\t5\t.\tAF=1;AQ=5;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\t1/1:21:4,15:3:5,1,0:..", + "chr16\t164839\tchr16_164839_G_GGT\tG\tGGT\t12\t.\tAF=1;AQ=12;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\t1/1:21:2,15:11:12,14,0:..", + "chr16\t164871\tchr16_164871_T_G\tT\tG\t6\t.\tAF=0.5;AQ=6;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\t0/1:20:12,7:7:6,0,24:..", + "chr16\t164884\tchr16_164884_G_GT\tG\tGT\t4\t.\tAF=1;AQ=4;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\t1/1:21:0,21:6:4,15,0:..", + "chr16\t164907\tchr16_164907_C_A\tC\tA\t15\t.\tAF=0.5;AQ=15;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\t0/1:20:12,8:15:15,0,22:..", + "chr16\t164931\tchr16_164931_C_G\tC\tG\t10\t.\tAF=0.5;AQ=10;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\t0/1:9:1,8:11:10,0,29:..", + "chr16\t164932\tchr16_164932_G_GGGCGGGC\tG\tGGGCGGGC\t6\t.\tAF=0.5;AQ=6;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\t0/1:9:2,7:7:6,0,21:..", + "chr16\t164942\tchr16_164942_G_GT\tG\tGT\t5\t.\tAF=0.5;AQ=5;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\t0/1:9:0,8:6:5,0,12:..", + "chr16\t164953\tchr16_164953_G_GGCGGC\tG\tGGCGGC\t5\t.\tAF=0.5;AQ=5;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\t0/1:21:14,6:7:5,0,24:..", + "chr16\t164985\tchr16_164985_C_CG\tC\tCG\t16\t.\tAF=1;AQ=16;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\t1/1:19:1,18:15:16,19,0:..", + "chr16\t165380\tchr16_165380_G_A\tG\tA\t25\t.\tAF=0.5;AQ=25;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\t0/1:22:14,8:25:25,0,40:..", + "chr16\t165856\tchr16_165856_G_C\tG\tC\t22\t.\tAF=0.5;AQ=22;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\t0/1:22:14,8:23:22,0,39:..", + "chr16\t166191\tchr16_166191_C_CG\tC\tCG\t12\t.\tAF=0.5;AQ=12;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\t0/1:22:14,6:13:12,0,32:..", + "chr16\t166518\tchr16_166518_TG_T\tTG\tT\t6\t.\tAF=0.5;AQ=6;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\t0/1:21:16,4:7:6,0,29:..", + "chr16\t167928\tchr16_167928_GT_G\tGT\tG\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|||||||||||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\t0/1:21:14,6:11:10,0,31:..", + "chr16\t167947\tchr16_167947_T_TC\tT\tTC\t16\t.\tAF=0.5;AQ=16;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\t0/1:21:11,10:15:16,0,20:..", + "chr16\t167948\tchr16_167948_T_C\tT\tC\t3\t.\tAF=0.5;AQ=3;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\t0/1:20:10,10:5:3,0,15:..", + "chr16\t168533\tchr16_168533_T_C\tT\tC\t25\t.\tAF=0.5;AQ=25;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\t0/1:20:11,9:25:25,0,41:..", + "chr16\t168736\tchr16_168736_A_G\tA\tG\t27\t.\tAF=0.5;AQ=27;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\t0/1:20:11,9:27:27,0,43:..", + "chr16\t169117\tchr16_169117_TG_T\tTG\tT\t2\t.\tAF=0.5;AQ=2;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\t0/1:20:17,3:5:2,0,24:..", + "chr16\t169624\tchr16_169624_TC_T\tTC\tT\t6\t.\tAF=0.5;AQ=6;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\t0/1:20:16,4:7:6,0,31:..", + "chr16\t170831\tchr16_170831_T_TCACA\tT\tTCACA\t5\t.\tAF=0.5;AQ=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\t0/1:20:6,6:5:20,0,24:..", + "chr16\t171206\tchr16_171206_T_TTTA\tT\tTTTA\t22\t.\tAF=0.5;AQ=22;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\t0/1:20:11,9:22:22,0,39:..", + "chr16\t171220\tchr16_171220_T_TATTA\tT\tTATTA\t3\t.\tAF=0.5;AQ=3;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\t0/1:20:16,4:5:3,0,24:..", + "chr16\t171534\tchr16_171534_AT_A\tAT\tA\t14\t.\tAF=0.5;AQ=14;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\t0/1:19:14,5:14:14,0,36:..", + "chr16\t171881\tchr16_171881_TC_T\tTC\tT\t19\t.\tAF=0.5;AQ=19;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\t0/1:19:12,7:19:19,0,33:..", + "chr16\t172288\tchr16_172288_AG_A\tAG\tA\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||587|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4391|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4415|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||601|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||2955|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4409|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||605|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||655|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4459|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1213|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:16,2:4:2,0,26:..", + "chr16\t172417\tchr16_172417_C_T\tC\tT\t18\t.\tAF=1;AQ=18;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||459|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4263|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4287|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||473|1||HGNC|HGNC:4824,T|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3083|1||HGNC|HGNC:4825,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4281|1||HGNC|HGNC:4823,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||477|1||HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||527|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,T|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4331|1||HGNC|HGNC:4823,T|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4896|-1|||,T|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1085|-1|||\tGT:DP:AD:GQ:PL:RNC\t1/1:19:0,19:15:18,17,0:..", + "chr16\t172418\tchr16_172418_T_C\tT\tC\t17\t.\tAF=1;AQ=17;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\t1/1:18:0,18:14:17,16,0:..", + "chr16\t172491\tchr16_172491_CG_C\tCG\tC\t2\t.\tAF=0.5;AQ=2;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|||||||||||384|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||4188|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||4212|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|||||||||||398|1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3158|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||4206|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|||||||||||402|1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||452|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||4256|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4821|-1|||,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||1010|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:17,2:4:2,0,25:..", + "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\t1/1:18:1,17:19:23,20,0:..", + "chr16\t172870\tchr16_172870_G_C\tG\tC\t18\t.\tAF=1;AQ=18;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\t1/1:18:0,18:15:18,17,0:..", + "chr16\t172906\tchr16_172906_AC_A\tAC\tA\t0\t.\tAF=0.5;AC=1;cadd_raw=-2;cadd_phred=-2;CSQ=-|5_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000251595|protein_coding|1/3||||32|||||||1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000320868|protein_coding|||||||||||3773|1||HGNC|HGNC:4823,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000397797|protein_coding|||||||||||3797|1||HGNC|HGNC:4823,-|5_prime_UTR_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000397806|protein_coding|1/3||||18|||||||1||HGNC|HGNC:4824,-|downstream_gene_variant|MODIFIER|HBAP1|ENSG00000225323|Transcript|ENST00000438841|unprocessed_pseudogene|||||||||||3573|1||HGNC|HGNC:4825,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000472694|retained_intron|||||||||||3791|1||HGNC|HGNC:4823,-|non_coding_transcript_exon_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000482565|retained_intron|1/2||||14|||||||1||HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA2|ENSG00000188536|Transcript|ENST00000484216|protein_coding|||||||||||37|1|cds_start_NF&cds_end_NF|HGNC|HGNC:4824,-|upstream_gene_variant|MODIFIER|HBA1|ENSG00000206172|Transcript|ENST00000487791|retained_intron|||||||||||3841|1||HGNC|HGNC:4823,-|downstream_gene_variant|MODIFIER||ENSG00000290010|Transcript|ENST00000702457|lncRNA|||||||||||4406|-1|||,-|downstream_gene_variant|MODIFIER||ENSG00000290038|Transcript|ENST00000702607|lncRNA|||||||||||595|-1|||\tGT:DP:AD:GQ:PL:RNC\t0/1:19:17,2:3:0,0,25:..", + "chr16\t173116\tchr16_173116_TC_T\tTC\tT\t2\t.\tAF=0.5;AQ=2;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\t0/1:19:16,3:4:2,0,27:..", + "chr16\t173707\tchr16_173707_A_G\tA\tG\t20\t.\tAF=1;AQ=20;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\t1/1:19:0,19:19:20,22,0:..", + "chr16\t274052\tchr16_274052_A_G\tA\tG\t19\t.\tAF=1;AQ=19;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\t1/1:32:0,32:17:19,21,0:..", + "chr16\t286660\tchr16_286660_G_A\tG\tA\t22\t.\tAF=1;AQ=22;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\t1/1:22:0,22:17:22,18,0:.." + ], + [ + "chr16\t346264\tchr16_346264_A_G\tA\tG\t21\t.\tAF=0.5;AQ=21;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\t0/1:26:15,11:22:21,0,39:..", + "chr16\t377013\tchr16_377013_G_C\tG\tC\t22\t.\tAF=0.5;AQ=22;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\t0/1:17:11,6:23:22,0,37:..", + "chr16\t520623\tchr16_520623_G_A\tG\tA\t27\t.\tAF=0.5;AQ=27;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\t0/1:18:9,9:28:27,0,45:..", + "chr16\t551632\tchr16_551632_T_C\tT\tC\t24\t.\tAF=1;AQ=24;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\t1/1:13:0,13:16:24,16,0:..", + "chr16\t582180\tchr16_582180_G_C\tG\tC\t16\t.\tAF=1;AQ=16;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\t1/1:6:0,6:9:16,8,0:..", + "chr16\t627629\tchr16_627629_T_C\tT\tC\t24\t.\tAF=1;AQ=24;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\t1/1:13:0,13:16:24,16,0:..", + "chr16\t638557\tchr16_638557_A_C\tA\tC\t21\t.\tAF=1;AQ=21;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\t1/1:14:0,14:15:21,16,0:..", + "chr16\t655844\tchr16_655844_T_C\tT\tC\t22\t.\tAF=1;AQ=22;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\t1/1:14:0,14:16:22,17,0:..", + "chr16\t667523\tchr16_667523_G_T\tG\tT\t21\t.\tAF=1;AQ=21;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\t1/1:22:0,22:17:21,18,0:..", + "chr16\t690466\tchr16_690466_A_G\tA\tG\t18\t.\tAF=1;AQ=18;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\t1/1:17:0,17:15:18,17,0:..", + "chr16\t723341\tchr16_723341_G_A\tG\tA\t18\t.\tAF=1;AQ=18;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\t1/1:17:0,17:16:18,18,0:..", + "chr16\t739761\tchr16_739761_A_G\tA\tG\t21\t.\tAF=1;AQ=21;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\t1/1:14:0,14:15:21,15,0:..", + "chr16\t766294\tchr16_766294_T_G\tT\tG\t25\t.\tAF=0.5;AQ=25;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\t0/1:19:12,7:25:25,0,44:..", + "chr16\t789996\tchr16_789996_T_C\tT\tC\t26\t.\tAF=0.5;AQ=26;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\t0/1:15:7,8:27:26,0,46:..", + "chr16\t813336\tchr16_813336_T_C\tT\tC\t30\t.\tAF=0.5;AQ=30;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\t0/1:14:5,9:30:30,0,41:..", + "chr16\t893361\tchr16_893361_T_C\tT\tC\t33\t.\tAF=0.5;AQ=33;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\t0/1:17:6,11:33:33,0,44:..", + "chr16\t947473\tchr16_947473_T_C\tT\tC\t17\t.\tAF=0.5;AQ=17;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\t0/1:23:8,15:17:17,0,38:..", + 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"chrX\t13785841\tchrX_13785841_C_T\tC\tT\t22\t.\tAF=1;AQ=22;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:14:22,14,0:..", + "chrX\t14581450\tchrX_14581450_A_G\tA\tG\t23\t.\tAF=1;AQ=23;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:16:0,16:15:23,15,0:..", + "chrX\t14609022\tchrX_14609022_T_C\tT\tC\t22\t.\tAF=1;AQ=22;AC=2;cadd_raw=-2;cadd_phred=-2;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||\tGT:DP:AD:GQ:PL:RNC\t1/1:14:0,14:15:22,16,0:.." + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T17:40:01.086742603" + } +} \ No newline at end of file diff --git a/subworkflows/local/snv_annotation/tests/nextflow.config b/subworkflows/local/snv_annotation/tests/nextflow.config index 37f927d4..2de8ad16 100644 --- a/subworkflows/local/snv_annotation/tests/nextflow.config +++ b/subworkflows/local/snv_annotation/tests/nextflow.config @@ -1,46 +1,71 @@ process { + withName: 'DEEPVARIANT' { + ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" } + ext.args = { [ + '--model_type WGS', + "--sample_name=${meta.id}", + '-vcf_stats_report=False' + ].join(' ') } + } + withName: 'GLNEXUS' { ext.args = '--config DeepVariant_unfiltered' } - withName: 'BCFTOOLS_CONCAT_GVCF' { - ext.prefix = { "${meta.id}_concat_gvcf" } - ext.args = '--no-version' - } - withName: 'BCFTOOLS_CONCAT_VCF' { - ext.prefix = { "${meta.id}_concat_vcf" } - ext.args = '--no-version' - } - withName: 'BCFTOOLS_SORT_GVCF' { - ext.prefix = { "${vcf}_sorted.g" } - } - withName: 'BCFTOOLS_SORT_VCF' { - ext.prefix = { "${vcf}_sorted" } - } - withName: 'BCFTOOLS_FILLTAGS' { - ext.prefix = { "${vcf}_filltags" } - ext.args = '--no-version' + + withName: 'BCFTOOLS_CONCAT' { + ext.prefix = { "${meta.id}_concat" } + ext.args = [ + '--no-version', + '--allow-overlaps' + ].join(' ') } - withName: 'BCFTOOLS_NORM' { - ext.prefix = { "${vcf}_norm" } + + withName: 'BCFTOOLS_NORM_MULTISAMPLE' { + ext.prefix = { "${meta.id}_norm_multisample" } ext.args = [ + '--no-version', '-m -', - '--output-type b', + '--output-type u', '--write-index=csi', + '-w 10000' + ].join(' ') + } + + withName: 'BCFTOOLS_NORM_SINGLESAMPLE' { + ext.prefix = { "${meta.id}_norm_singlesample" } + ext.args = [ + '--no-version', + '-m -', '-w 10000', - '--no-version' + '--output-type u', ].join(' ') } - withName: 'DEEPVARIANT' { - ext.args = '--model_type PACBIO' + + withName: '.*:SHORT_VARIANT_CALLING:BCFTOOLS_FILLTAGS' { + ext.prefix = { "${meta.id}_ac" } + ext.args = [ + '--no-version', + '--output-type u' + ].join(' ') } + + withName: 'BCFTOOLS_FILLTAGS_ANNO' { + ext.prefix = { "${meta.id}_filltags_anno" } + ext.args = [ + '--no-version', + '--output-type z' + ].join(' ') + } + withName: 'MINIMAP2_ALIGN' { ext.args = '-x map-hifi' } + withName: 'ENSEMBLVEP_VEP' { - ext.args = [ + ext.args = { [ + '--offline', '--vcf', - '--compress_output bgzip', - '--offline' - ].join(' ') + '--compress_output bgzip' + ].join(' ') } } } diff --git a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf index 93003674..d55e598d 100644 --- a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf @@ -43,6 +43,7 @@ def workflowSkips = [ call_paralogs : "skip_call_paralogs", cnv_calling : "skip_cnv_calling", phasing : "skip_phasing_wf", + rank_variants : "skip_rank_variants", repeat_calling : "skip_repeat_calling", repeat_annotation: "skip_repeat_annotation", methylation : "skip_methylation_wf", @@ -58,6 +59,7 @@ def workflowDependencies = [ snv_annotation : ["mapping", "snv_calling"], cnv_calling : ["mapping", "snv_calling"], phasing : ["mapping", "snv_calling"], + rank_variants : ["mapping", "snv_calling", "snv_annotation"], repeat_calling : ["mapping", "snv_calling", "phasing"], repeat_annotation: ["mapping", "snv_calling", "phasing", "repeat_calling"], methylation : ["mapping", "snv_calling", "phasing"], @@ -80,6 +82,7 @@ def parameterStatus = [ skip_short_variant_calling: params.skip_short_variant_calling, skip_phasing_wf : params.skip_phasing_wf, skip_methylation_wf : params.skip_methylation_wf, + skip_rank_variants : params.skip_rank_variants, skip_repeat_calling : params.skip_repeat_calling, skip_repeat_annotation : params.skip_repeat_annotation, skip_snv_annotation : params.skip_snv_annotation, @@ -185,6 +188,16 @@ workflow PIPELINE_INITIALISATION { } .set { ch_samplesheet } + // Check that there's samples with affected phenotype if we are ranking variants + ch_samplesheet + .filter { meta, reads -> meta.phenotype == 2 } + .ifEmpty { + if(!params.skip_rank_variants) { + error("No samples in samplesheet has affected phenotype (=2), --skip_rank_variants has to be active.") + } + } + + emit: samplesheet = ch_samplesheet versions = ch_versions diff --git a/tests/main.nf.test b/tests/main.nf.test index 14f7020a..66c8b58a 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -88,20 +88,16 @@ nextflow_pipeline { bam("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_spanning_sorted.bam", stringency: 'silent').getReadsMD5(), ).match() }, // Assert exists multisample + { assert new File("$outputDir/databases/echtvar/encode/multisample/multisample.zip").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_data.json").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc.log").exists() }, { assert new File("$outputDir/multiqc/multiqc_report.html").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() }, - { assert new File("$outputDir/ranked_variants/multisample_snv_ranked.vcf.gz").exists() }, - { assert new File("$outputDir/ranked_variants/multisample_snv_ranked.vcf.gz.tbi").exists() }, { assert new File("$outputDir/repeat_calling/trgt/multi_sample/multisample/multisample.vcf.gz").exists() }, { assert new File("$outputDir/repeat_calling/trgt/multi_sample/multisample/multisample.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_annotation/echtvar/encode/multisample/multisample.zip").exists() }, - { assert new File("$outputDir/snv_annotation/vep/multi_sample/multisample/multisample_vep.vcf.gz").exists() }, - { assert new File("$outputDir/snv_annotation/vep/multi_sample/multisample/multisample_vep.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_calling/multi_sample/glnexus/multisample/multisample.bcf.gz").exists() }, - { assert new File("$outputDir/snv_calling/multi_sample/glnexus/multisample/multisample.bcf.gz.csi").exists() }, + { assert new File("$outputDir/snvs/multi_sample/multisample/multisample_snv_annotated_ranked.vcf.gz").exists() }, + { assert new File("$outputDir/snvs/multi_sample/multisample/multisample_snv_annotated_ranked.vcf.gz.tbi").exists() }, { assert new File("$outputDir/sv_calling/sniffles/multi_sample/multisample_sniffles.vcf.gz").exists() }, { assert new File("$outputDir/sv_calling/sniffles/multi_sample/multisample_sniffles.vcf.gz.tbi").exists() }, // Assert exists HG002_Revio @@ -133,12 +129,8 @@ nextflow_pipeline { { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio/HG002_Revio_repeat_expansion_stranger.vcf.gz").exists() }, { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio/HG002_Revio_repeat_expansion_stranger.vcf.gz.tbi").exists() }, { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio/HG002_Revio_spanning_sorted.bam.bai").exists() }, - { assert new File("$outputDir/snv_annotation/vep/single_sample/HG002_Revio.vcf.gz").exists() }, - { assert new File("$outputDir/snv_annotation/vep/single_sample/HG002_Revio.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/gvcf/HG002_Revio/HG002_Revio_sorted.g.vcf.gz").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/gvcf/HG002_Revio/HG002_Revio_sorted.g.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/vcf/HG002_Revio/HG002_Revio_sorted.vcf.gz").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/vcf/HG002_Revio/HG002_Revio_sorted.vcf.gz.tbi").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("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.snf").exists() }, { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.vcf.gz").exists() }, { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio/HG002_Revio_sniffles.vcf.gz.tbi").exists() } @@ -262,6 +254,7 @@ nextflow_pipeline { bam("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_spanning_sorted.bam", stringency: 'silent').getReadsMD5(), ).match() }, // Assert exists multisample - note the trgt multisample that doesn't exist in singlesample + { assert new File("$outputDir/databases/echtvar/encode/multisample/multisample.zip").exists() }, { assert new File("$outputDir/qc_aligned_reads/somalier/relate/multisample/multisample.pairs.tsv").exists() }, { assert new File("$outputDir/qc_aligned_reads/somalier/relate/multisample/multisample.samples.tsv").exists() }, { assert new File("$outputDir/qc_aligned_reads/somalier/relate/multisample/multisample.html").exists() }, @@ -271,13 +264,8 @@ nextflow_pipeline { { assert new File("$outputDir/multiqc/multiqc_report.html").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() }, { assert new File("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt").exists() }, - { assert new File("$outputDir/ranked_variants/multisample_snv_ranked.vcf.gz").exists() }, - { assert new File("$outputDir/ranked_variants/multisample_snv_ranked.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_annotation/echtvar/encode/multisample/multisample.zip").exists() }, - { assert new File("$outputDir/snv_annotation/vep/multi_sample/multisample/multisample_vep.vcf.gz").exists() }, - { assert new File("$outputDir/snv_annotation/vep/multi_sample/multisample/multisample_vep.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_calling/multi_sample/glnexus/multisample//multisample.bcf.gz").exists() }, - { assert new File("$outputDir/snv_calling/multi_sample/glnexus/multisample/multisample.bcf.gz.csi").exists() }, + { assert new File("$outputDir/snvs/multi_sample/multisample/multisample_snv_annotated_ranked.vcf.gz").exists() }, + { assert new File("$outputDir/snvs/multi_sample/multisample/multisample_snv_annotated_ranked.vcf.gz.tbi").exists() }, { assert new File("$outputDir/sv_calling/sniffles/multi_sample/multisample_sniffles.vcf.gz").exists() }, { assert new File("$outputDir/sv_calling/sniffles/multi_sample/multisample_sniffles.vcf.gz.tbi").exists() }, { assert new File("$outputDir/repeat_calling/trgt/multi_sample/multisample/multisample.vcf.gz").exists() }, @@ -311,12 +299,8 @@ nextflow_pipeline { { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_A/HG002_Revio_A_repeat_expansion_stranger.vcf.gz").exists() }, { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_A/HG002_Revio_A_repeat_expansion_stranger.vcf.gz.tbi").exists() }, { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_A/HG002_Revio_A_spanning_sorted.bam.bai").exists() }, - { assert new File("$outputDir/snv_annotation/vep/single_sample/HG002_Revio_A.vcf.gz").exists() }, - { assert new File("$outputDir/snv_annotation/vep/single_sample/HG002_Revio_A.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/gvcf/HG002_Revio_A/HG002_Revio_A_sorted.g.vcf.gz").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/gvcf/HG002_Revio_A/HG002_Revio_A_sorted.g.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/vcf/HG002_Revio_A/HG002_Revio_A_sorted.vcf.gz").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/vcf/HG002_Revio_A/HG002_Revio_A_sorted.vcf.gz.tbi").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("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.snf").exists() }, { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.vcf.gz").exists() }, { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_A/HG002_Revio_A_sniffles.vcf.gz.tbi").exists() }, @@ -348,12 +332,8 @@ nextflow_pipeline { { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_B/HG002_Revio_B_repeat_expansion_stranger.vcf.gz").exists() }, { assert new File("$outputDir/repeat_annotation/stranger/HG002_Revio_B/HG002_Revio_B_repeat_expansion_stranger.vcf.gz.tbi").exists() }, { assert new File("$outputDir/repeat_calling/trgt/single_sample/HG002_Revio_B/HG002_Revio_B_spanning_sorted.bam.bai").exists() }, - { assert new File("$outputDir/snv_annotation/vep/single_sample/HG002_Revio_B.vcf.gz").exists() }, - { assert new File("$outputDir/snv_annotation/vep/single_sample/HG002_Revio_B.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/gvcf/HG002_Revio_B/HG002_Revio_B_sorted.g.vcf.gz").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/gvcf/HG002_Revio_B/HG002_Revio_B_sorted.g.vcf.gz.tbi").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/vcf/HG002_Revio_B/HG002_Revio_B_sorted.vcf.gz").exists() }, - { assert new File("$outputDir/snv_calling/single_sample/deepvariant/vcf/HG002_Revio_B/HG002_Revio_B_sorted.vcf.gz.tbi").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("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.snf").exists() }, { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.vcf.gz").exists() }, { assert new File("$outputDir/sv_calling/sniffles/single_sample/HG002_Revio_B/HG002_Revio_B_sniffles.vcf.gz.tbi").exists() } diff --git a/workflows/nallo.nf b/workflows/nallo.nf index c44d7eb4..f8684d57 100644 --- a/workflows/nallo.nf +++ b/workflows/nallo.nf @@ -37,6 +37,7 @@ include { FQCRS } from '../modules/local/fqcrs' 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 { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' include { FASTQC } from '../modules/nf-core/fastqc/main' @@ -60,6 +61,7 @@ workflow NALLO { ch_input main: + ch_vep_cache = Channel.value([]) ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() @@ -80,7 +82,6 @@ workflow NALLO { : '' ch_variant_catalog = params.variant_catalog ? Channel.fromPath(params.variant_catalog).map { it -> [ it.simpleName, it ] }.collect() : '' - // TODO: Add all missing parameters to schema ch_databases = params.snp_db ? Channel.fromSamplesheet('snp_db', immutable_meta: false).map{ it[1] }.collect() : '' ch_variant_consequences_snv = params.variant_consequences_snv ? Channel.fromPath(params.variant_consequences_snv).collect() @@ -102,9 +103,7 @@ workflow NALLO { // Check parameter that doesn't conform to schema validation here if (params.split_fastq != 0 && (params.split_fastq < 2 || params.split_fastq > 999 )) { error "--split_fastq must be 0, or between 2 and 999."} - if (params.parallel_snv == 0 ) { error "--parallel_snv must be > 0." } if (params.phaser.matches('hiphase_sv|hiphase_snv') && 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" } - // Create PED from samplesheet ch_pedfile = ch_input.toList().map { file(CustomFunctions.makePed(it, params.outdir)) } @@ -152,6 +151,17 @@ workflow NALLO { ) ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) + if(!params.skip_snv_annotation) { + + if (params.vep_cache) { + if (params.vep_cache.endsWith("tar.gz")) { + ch_vep_cache = PREPARE_GENOME.out.vep_resources + } else { + ch_vep_cache = Channel.fromPath(params.vep_cache).collect() + } + } + } + // Gather indices fasta = PREPARE_GENOME.out.fasta fai = PREPARE_GENOME.out.fai @@ -270,56 +280,28 @@ workflow NALLO { ch_versions = ch_versions.mix(STRUCTURAL_VARIANT_CALLING.out.versions) if(!params.skip_short_variant_calling) { - // Call SNVs with DeepVariant + + // + // This calls and outputs a merged and normalised VCF per sample, + // to be used in downstream subworkflows requiring SNVs. + // This also outputs a merged multisample VCFs _per region_, to be used in annotation and ranking SHORT_VARIANT_CALLING( ch_snv_calling_in, fasta, fai, SCATTER_GENOME.out.bed ) ch_versions = ch_versions.mix(SHORT_VARIANT_CALLING.out.versions) if(!params.skip_snv_annotation) { - def ch_vep_cache - - if (params.vep_cache) { - if (params.vep_cache.endsWith("tar.gz")) { - ch_vep_cache = PREPARE_GENOME.out.vep_resources - } else { - ch_vep_cache = Channel.fromPath(params.vep_cache).collect() - } - } else { - ch_vep_cache = Channel.value([]) - } - - // - // Make a echtvar file of all samples, and combine with input databases - // - ECHTVAR_ENCODE ( SHORT_VARIANT_CALLING.out.combined_bcf ) - ch_versions = ch_versions.mix(ECHTVAR_ENCODE.out.versions) - - ch_databases - .concat ( ECHTVAR_ENCODE.out.db.map { it[1] } ) - .collect() - .set { snv_annotation_dbs } - // - // Annotate a multisample VCF + // Annotate one multisample VCF per variant call region // SNV_ANNOTATION( SHORT_VARIANT_CALLING.out.combined_bcf, - snv_annotation_dbs, + ch_databases, fasta, ch_vep_cache, params.vep_cache_version ) ch_versions = ch_versions.mix(SNV_ANNOTATION.out.versions) - // Split multisample VCF to also publish a VCF per sample - BCFTOOLS_PLUGINSPLIT ( - SNV_ANNOTATION.out.vcf.join( SNV_ANNOTATION.out.tbi ), - [], - [], - [], - [] - ) - ANN_CSQ_PLI_SNV ( SNV_ANNOTATION.out.vcf, ch_variant_consequences_snv @@ -327,18 +309,67 @@ workflow NALLO { ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions) ANN_CSQ_PLI_SNV.out.vcf_ann - .filter { meta, vcf -> meta.contains_affected } - .set { ch_rank_variants_in } + .join( ANN_CSQ_PLI_SNV.out.tbi_ann ) + .set { ch_vcf_tbi } + } else { + SHORT_VARIANT_CALLING.out.combined_bcf + .join( SHORT_VARIANT_CALLING.out.combined_csi ) + .set { ch_vcf_tbi } + } - // Only run on if we have affected individuals + ch_vcf_tbi + .map { meta, vcf, tbi -> + new_meta = [ + id:'multisample', + contains_affected: meta.contains_affected.any() + ] + [ new_meta, vcf, tbi ] + } + .groupTuple() + .set { ch_bcftools_concat_in } + + // Concat into a mutlisample VCF with all regions + // Pubish from here if we don't run rank variants + BCFTOOLS_CONCAT ( ch_bcftools_concat_in ) + ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions) + + // Make an echtvar database of all samples + ECHTVAR_ENCODE ( BCFTOOLS_CONCAT.out.vcf ) + ch_versions = ch_versions.mix(ECHTVAR_ENCODE.out.versions) + + if(!params.skip_snv_annotation && !params.skip_rank_variants) { + // Only run if we have affected individuals + // Publish from here if we have affected individuals + // Not sure if this could be run in parallel or not RANK_VARIANTS_SNV ( - ch_rank_variants_in, + BCFTOOLS_CONCAT.out.vcf.filter { meta, vcf -> meta.contains_affected }, ch_pedfile, ch_reduced_penetrance, ch_score_config_snv ) ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions) + + split_multisample_in = Channel.empty() + + // If there are affected individuals and RANK_VARIANTS has been run, + // split that, otherwise grab the VCF that should have gone into RANK_VARIANTS + split_multisample_in = split_multisample_in + .mix( + RANK_VARIANTS_SNV.out.vcf + .join( RANK_VARIANTS_SNV.out.tbi ) + .filter { meta, vcf, tbi -> meta.contains_affected } + ) + .mix( BCFTOOLS_CONCAT.out.vcf + .join( BCFTOOLS_CONCAT.out.tbi ) + .filter { meta, vcf, tbi -> !meta.contains_affected } + ) + } else { + BCFTOOLS_CONCAT.out.vcf + .join( BCFTOOLS_CONCAT.out.tbi ) + .set { split_multisample_in } } + // Split multisample VCF to also publish a VCF per sample + BCFTOOLS_PLUGINSPLIT ( split_multisample_in, [], [], [], [] ) if(!params.skip_cnv_calling) { bam_bai @@ -356,7 +387,6 @@ workflow NALLO { ch_versions = ch_versions.mix(PHASING.out.versions) hap_bam_bai = PHASING.out.haplotagged_bam_bai - if(!params.skip_methylation_wf) { // Pileup methylation with modkit METHYLATION( hap_bam_bai, fasta, fai, ch_input_bed )