From 22ae6c5d9c2a14206d04aae7838d7d760c3c43b7 Mon Sep 17 00:00:00 2001 From: Mark Walker Date: Mon, 8 Jan 2024 18:45:04 +0000 Subject: [PATCH] Update docker images list, triggered by 6077c312 Add json template Update top-level workflows; concat variant lists Fix contig list read Update ref panel outputs; fix CleanVcf template Fix Terra CleanVcf templates --- .../CleanVcf.json.tmpl | 4 +- .../test/MakeCohortVcf/CleanVcf.json.tmpl | 4 +- inputs/values/ref_panel_1kg.json | 252 +++++++----------- wdl/CleanVcf.wdl | 8 +- wdl/GATKSVPipelineBatch.wdl | 4 +- wdl/GATKSVPipelineSingleSample.wdl | 4 + wdl/MakeCohortVcf.wdl | 15 +- wdl/ReshardVcf.wdl | 7 +- wdl/ResolveComplexVariants.wdl | 41 ++- 9 files changed, 166 insertions(+), 173 deletions(-) diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl index c6ffd5dd1..e7c1bc7a0 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl @@ -19,7 +19,7 @@ "CleanVcf.cohort_name": "${this.sample_set_set_id}", "CleanVcf.ped_file": "${workspace.cohort_ped_file}", "CleanVcf.complex_genotype_vcfs": "${this.complex_genotype_vcfs}", - "CleanVcf.complex_resolve_bothside_pass_lists": "${this.complex_resolve_bothside_pass_lists}", - "CleanVcf.complex_resolve_background_fail_lists": "${this.complex_resolve_background_fail_lists}" + "CleanVcf.complex_resolve_bothside_pass_list": "${this.complex_resolve_bothside_pass_list}", + "CleanVcf.complex_resolve_background_fail_list": "${this.complex_resolve_background_fail_list}" } diff --git a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl index 0d43fc3ac..8606a4a50 100644 --- a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl +++ b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl @@ -19,6 +19,6 @@ "CleanVcf.cohort_name": {{ test_batch.name | tojson }}, "CleanVcf.ped_file": {{ test_batch.ped_file | tojson }}, "CleanVcf.complex_genotype_vcfs": {{ test_batch.complex_genotype_vcfs | tojson }}, - "CleanVcf.complex_resolve_bothside_pass_lists": {{ test_batch.complex_resolve_bothside_pass_lists | tojson }}, - "CleanVcf.complex_resolve_background_fail_lists": {{ test_batch.complex_resolve_background_fail_lists | tojson }} + "CleanVcf.complex_resolve_bothside_pass_list": {{ test_batch.complex_resolve_bothside_pass_list | tojson }}, + "CleanVcf.complex_resolve_background_fail_list": {{ test_batch.complex_resolve_background_fail_list | tojson }} } diff --git a/inputs/values/ref_panel_1kg.json b/inputs/values/ref_panel_1kg.json index 5cb0ccd82..bec57125e 100644 --- a/inputs/values/ref_panel_1kg.json +++ b/inputs/values/ref_panel_1kg.json @@ -1166,8 +1166,8 @@ "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/breakpoint-overlap-dropped-record-vcfs/ref_panel_1kg.chrX.breakpoint_overlap.dropped_records.vcf.gz.tbi", "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/breakpoint-overlap-dropped-record-vcfs/ref_panel_1kg.chrY.breakpoint_overlap.dropped_records.vcf.gz.tbi" ], - "clean_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/MakeCohortVcf/8a209488-c928-449d-92cd-0a5131e92b7c/call-CleanVcf/CleanVcf/277f3f25-bb99-4fe4-a48b-567fd3f344f9/call-ConcatCleanedVcfs/ref_panel_1kg.cleaned.vcf.gz", - "clean_vcf_index": "gs://gatk-sv-ref-panel-1kg/outputs/MakeCohortVcf/8a209488-c928-449d-92cd-0a5131e92b7c/call-CleanVcf/CleanVcf/277f3f25-bb99-4fe4-a48b-567fd3f344f9/call-ConcatCleanedVcfs/ref_panel_1kg.cleaned.vcf.gz.tbi", + "clean_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.cleaned.vcf.gz", + "clean_vcf_index": "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.cleaned.vcf.gz.tbi", "clean_vcf_gatk_formatter_args": "", "cluster_background_fail_lists": [ "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/CombineBatches/cluster-background-fail-lists/ref_panel_1kg.chr1.sr_background_fail.updated2.txt", @@ -1278,160 +1278,110 @@ "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/CombineBatches/combined-vcfs/ref_panel_1kg.chrY.concat_pesr_depth.vcf.gz.tbi" ], "complex_genotype_vcfs": [ - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr1.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr2.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr3.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr4.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr5.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr6.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr7.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr8.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr9.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr10.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr11.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr12.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr13.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr14.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr15.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr16.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr17.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr18.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr19.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr20.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr21.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr22.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chrX.regenotyped.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chrY.regenotyped.vcf.gz" + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr1.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr2.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr3.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr4.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr5.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr6.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr7.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr8.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr9.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr10.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr11.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr12.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr13.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr14.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr15.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr16.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr17.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr18.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr19.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr20.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr21.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr22.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chrX.regenotyped.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chrY.regenotyped.vcf.gz" ], "complex_genotype_vcf_indexes": [ - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr1.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr2.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr3.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr4.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr5.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr6.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr7.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr8.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr9.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr10.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr11.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr12.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr13.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr14.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr15.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr16.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr17.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr18.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr19.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr20.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr21.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chr22.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chrX.regenotyped.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/GenotypeComplexVariants/complex-genotype-vcfs/ref_panel_1kg.chrY.regenotyped.vcf.gz.tbi" - ], - "complex_resolve_bothside_pass_lists": [ - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr1.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr2.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr3.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr4.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr5.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr6.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr7.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr8.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr9.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr10.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr11.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr12.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr13.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr14.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr15.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr16.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr17.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr18.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr19.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr20.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr21.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chr22.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chrX.sr_bothside_pass.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-bothside-pass-lists/ref_panel_1kg.chrY.sr_bothside_pass.updated3.txt" - ], - "complex_resolve_background_fail_lists": [ - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr1.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr2.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr3.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr4.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr5.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr6.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr7.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr8.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr9.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr10.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr11.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr12.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr13.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr14.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr15.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr16.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr17.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr18.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr19.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr20.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr21.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chr22.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chrX.sr_background_fail.updated3.txt", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-background-fail-lists/ref_panel_1kg.chrY.sr_background_fail.updated3.txt" + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr1.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr2.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr3.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr4.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr5.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr6.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr7.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr8.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr9.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr10.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr11.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr12.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr13.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr14.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr15.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr16.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr17.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr18.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr19.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr20.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr21.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chr22.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chrX.regenotyped.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.chrY.regenotyped.vcf.gz.tbi" ], + "complex_resolve_bothside_pass_list": "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.all.sr_bothside_pass.updated3.txt", + "complex_resolve_background_fail_list": "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.all.sr_background_fail.updated3.txt", "complex_resolve_vcfs": [ - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr1.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr2.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr3.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr4.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr5.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr6.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr7.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr8.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr9.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr10.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr11.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr12.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr13.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr14.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr15.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr16.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr17.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr18.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr19.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr20.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr21.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr22.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chrX.renamed.vcf.gz", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chrY.renamed.vcf.gz" + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr1.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr2.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr3.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr4.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr5.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr6.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr7.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr8.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr9.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr10.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr11.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr12.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr13.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr14.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr15.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr16.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr17.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr18.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr19.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr20.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr21.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr22.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chrX.resharded.vcf.gz", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chrY.resharded.vcf.gz" ], "complex_resolve_vcf_indexes": [ - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr1.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr2.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr3.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr4.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr5.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr6.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr7.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr8.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr9.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr10.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr11.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr12.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr13.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr14.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr15.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr16.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr17.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr18.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr19.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr20.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr21.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chr22.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chrX.renamed.vcf.gz.tbi", - "gs://gatk-sv-ref-panel-1kg/outputs/mw-make-cohort-vcf-templates/ResolveComplexVariants/complex-resolve-vcfs/ref_panel_1kg.chrY.renamed.vcf.gz" + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr1.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr2.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr3.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr4.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr5.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr6.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr7.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr8.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr9.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr10.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr11.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr12.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr13.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr14.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr15.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr16.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr17.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr18.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr19.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr20.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr21.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chr22.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chrX.resharded.vcf.gz.tbi", + "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/ref_panel_1kg.reshard_vcf.chrY.resharded.vcf.gz.tbi" ], "concordance_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/mw_sv_concordance_update/ref_panel_1kg.concordance.vcf.gz", "concordance_vcf_index": "gs://gatk-sv-ref-panel-1kg/outputs/mw_sv_concordance_update/ref_panel_1kg.concordance.vcf.gz.tbi", @@ -2557,7 +2507,7 @@ "merged_wham_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-ClusterBatch/ClusterBatch/52feaa2f-66f2-457f-93d9-8967bc4cba83/call-ClusterPESR_wham/ClusterPESR/27daacc4-6b74-4a06-b8c2-1180494bbbdb/call-ConcatVCFs/cacheCopy/ref_panel_1kg.wham.vcf.gz", "merged_wham_vcf_index": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-ClusterBatch/ClusterBatch/52feaa2f-66f2-457f-93d9-8967bc4cba83/call-ClusterPESR_wham/ClusterPESR/27daacc4-6b74-4a06-b8c2-1180494bbbdb/call-ConcatVCFs/cacheCopy/ref_panel_1kg.wham.vcf.gz.tbi", "metrics_file_batch": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-CatBatchMetrics/cacheCopy/batch_sv.ref_panel_1kg.metrics.tsv", - "metrics_file_makecohortvcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-MakeCohortVcf/MakeCohortVcf/bfd4ef15-d9ea-437b-ade4-bc08e79c29a8/call-MakeCohortVcfMetrics/MakeCohortVcfMetrics/799d5a40-3833-47c5-94c5-fe90a5d65c24/call-CatMetrics/cacheCopy/MakeCohortVcf.ref_panel_1kg.metrics.tsv", + "metrics_file_makecohortvcf": "gs://gatk-sv-ref-panel-1kg/outputs/mw-vcf-reshard/MakeCohortVcf.ref_panel_1kg.metrics.tsv", "name": "ref_panel_1kg", "outlier_cutoff_table": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v1/module03_outlier_cutoff_table.tsv", "ped_file": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/ped/1kg_ref_panel_v1.ped", diff --git a/wdl/CleanVcf.wdl b/wdl/CleanVcf.wdl index 6c00358b2..c86e88500 100644 --- a/wdl/CleanVcf.wdl +++ b/wdl/CleanVcf.wdl @@ -11,8 +11,8 @@ workflow CleanVcf { String cohort_name Array[File] complex_genotype_vcfs - Array[File] complex_resolve_bothside_pass_lists - Array[File] complex_resolve_background_fail_lists + File complex_resolve_bothside_pass_list + File complex_resolve_background_fail_list File ped_file File contig_list @@ -118,9 +118,9 @@ workflow CleanVcf { input: vcf=complex_genotype_vcfs[i], contig=contig, - background_list=complex_resolve_background_fail_lists[i], + background_list=complex_resolve_background_fail_list, ped_file=ped_file, - bothsides_pass_list=complex_resolve_bothside_pass_lists[i], + bothsides_pass_list=complex_resolve_bothside_pass_list, allosome_fai=allosome_fai, prefix="~{cohort_name}.~{contig}", max_shards_per_chrom_step1=max_shards_per_chrom_step1, diff --git a/wdl/GATKSVPipelineBatch.wdl b/wdl/GATKSVPipelineBatch.wdl index abe308273..e328806bc 100644 --- a/wdl/GATKSVPipelineBatch.wdl +++ b/wdl/GATKSVPipelineBatch.wdl @@ -452,8 +452,8 @@ workflow GATKSVPipelineBatch { # ResolveComplexVariants Array[File] complex_resolve_vcfs = MakeCohortVcf.complex_resolve_vcfs Array[File] complex_resolve_vcf_indexes = MakeCohortVcf.complex_resolve_vcf_indexes - Array[File] complex_resolve_bothside_pass_lists = MakeCohortVcf.complex_resolve_bothside_pass_lists - Array[File] complex_resolve_background_fail_lists = MakeCohortVcf.complex_resolve_background_fail_lists + File complex_resolve_bothside_pass_list = MakeCohortVcf.complex_resolve_bothside_pass_list + File complex_resolve_background_fail_list = MakeCohortVcf.complex_resolve_background_fail_list Array[File] breakpoint_overlap_dropped_record_vcfs = MakeCohortVcf.breakpoint_overlap_dropped_record_vcfs Array[File] breakpoint_overlap_dropped_record_vcf_indexes = MakeCohortVcf.breakpoint_overlap_dropped_record_vcf_indexes diff --git a/wdl/GATKSVPipelineSingleSample.wdl b/wdl/GATKSVPipelineSingleSample.wdl index 9125f9238..d9e55d5e6 100644 --- a/wdl/GATKSVPipelineSingleSample.wdl +++ b/wdl/GATKSVPipelineSingleSample.wdl @@ -440,6 +440,8 @@ workflow GATKSVPipelineSingleSample { RuntimeAttr? runtime_override_update_sr_list_fail RuntimeAttr? runtime_override_breakpoint_overlap_filter RuntimeAttr? runtime_override_concat_resolve + RuntimeAttr? runtime_override_concat_bothside_pass + RuntimeAttr? runtime_override_concat_background_fail RuntimeAttr? runtime_override_get_se_cutoff RuntimeAttr? runtime_override_shard_vcf_cpx @@ -1192,6 +1194,8 @@ workflow GATKSVPipelineSingleSample { runtime_override_update_sr_list_fail=runtime_override_update_sr_list_fail, runtime_override_subset_inversions=runtime_override_subset_inversions, runtime_override_concat_resolve=runtime_override_concat_resolve, + runtime_override_concat_bothside_pass=runtime_override_concat_bothside_pass, + runtime_override_concat_background_fail=runtime_override_concat_background_fail, runtime_override_get_se_cutoff=runtime_override_get_se_cutoff, runtime_override_shard_vcf_cpx=runtime_override_shard_vcf_cpx, runtime_override_shard_vids_resolve=runtime_override_shard_vids_resolve, diff --git a/wdl/MakeCohortVcf.wdl b/wdl/MakeCohortVcf.wdl index ac8390ebb..5ea66ea50 100644 --- a/wdl/MakeCohortVcf.wdl +++ b/wdl/MakeCohortVcf.wdl @@ -122,6 +122,8 @@ workflow MakeCohortVcf { RuntimeAttr? runtime_override_update_sr_list_pass RuntimeAttr? runtime_override_update_sr_list_fail RuntimeAttr? runtime_override_concat_resolve + RuntimeAttr? runtime_override_concat_bothside_pass + RuntimeAttr? runtime_override_concat_background_fail RuntimeAttr? runtime_override_get_se_cutoff RuntimeAttr? runtime_override_shard_vcf_cpx @@ -146,6 +148,9 @@ workflow MakeCohortVcf { RuntimeAttr? runtime_override_hail_merge_resolve_inv RuntimeAttr? runtime_override_fix_header_resolve_inv + # overrides for ReshardVcf + RuntimeAttr? runtime_override_reshard + # overrides for GenotypeComplexContig RuntimeAttr? runtime_override_ids_from_median RuntimeAttr? runtime_override_split_vcf_to_genotype @@ -300,6 +305,8 @@ workflow MakeCohortVcf { runtime_override_breakpoint_overlap_filter=runtime_override_breakpoint_overlap_filter, runtime_override_subset_inversions=runtime_override_subset_inversions, runtime_override_concat=runtime_override_concat_resolve, + runtime_override_concat_bothside_pass=runtime_override_concat_bothside_pass, + runtime_override_concat_background_fail=runtime_override_concat_background_fail, runtime_override_get_se_cutoff=runtime_override_get_se_cutoff, runtime_override_shard_vcf_cpx=runtime_override_shard_vcf_cpx, @@ -364,8 +371,8 @@ workflow MakeCohortVcf { input: cohort_name=cohort_name, complex_genotype_vcfs=GenotypeComplexVariants.complex_genotype_vcfs, - complex_resolve_bothside_pass_lists=ResolveComplexVariants.complex_resolve_bothside_pass_lists, - complex_resolve_background_fail_lists=ResolveComplexVariants.complex_resolve_background_fail_lists, + complex_resolve_bothside_pass_list=ResolveComplexVariants.complex_resolve_bothside_pass_list, + complex_resolve_background_fail_list=ResolveComplexVariants.complex_resolve_background_fail_list, ped_file=ped_file, contig_list=contig_list, allosome_fai=allosome_fai, @@ -495,8 +502,8 @@ workflow MakeCohortVcf { # ResolveComplexVariants Array[File] complex_resolve_vcfs = ResolveComplexVariants.complex_resolve_vcfs Array[File] complex_resolve_vcf_indexes = ResolveComplexVariants.complex_resolve_vcf_indexes - Array[File] complex_resolve_bothside_pass_lists = ResolveComplexVariants.complex_resolve_bothside_pass_lists - Array[File] complex_resolve_background_fail_lists = ResolveComplexVariants.complex_resolve_background_fail_lists + File complex_resolve_bothside_pass_list = ResolveComplexVariants.complex_resolve_bothside_pass_list + File complex_resolve_background_fail_list = ResolveComplexVariants.complex_resolve_background_fail_list Array[File] breakpoint_overlap_dropped_record_vcfs = ResolveComplexVariants.breakpoint_overlap_dropped_record_vcfs Array[File] breakpoint_overlap_dropped_record_vcf_indexes = ResolveComplexVariants.breakpoint_overlap_dropped_record_vcf_indexes diff --git a/wdl/ReshardVcf.wdl b/wdl/ReshardVcf.wdl index 03969d269..b01309b71 100644 --- a/wdl/ReshardVcf.wdl +++ b/wdl/ReshardVcf.wdl @@ -3,12 +3,11 @@ version 1.0 import "Structs.wdl" import "TasksMakeCohortVcf.wdl" as MiniTasks -# Consumes a contig-sharded vcf where some shards may contain a small proportion of records from other -# contigs and moves them to their correct shards. +# Consumes a set of vcfs and distributes them into contig shards workflow ReshardVcf { input { - Array[File] vcfs # Must be sorted and indexed + Array[File] vcfs # Order does not matter but must be sorted and indexed File contig_list String prefix Boolean? use_ssd @@ -16,7 +15,7 @@ workflow ReshardVcf { RuntimeAttr? runtime_override_reshard } - Array[String] contigs = read_lines(contig_list) + Array[String] contigs = transpose(read_tsv(contig_list))[0] scatter (i in range(length(vcfs))) { File vcf_indexes = vcfs[i] + ".tbi" diff --git a/wdl/ResolveComplexVariants.wdl b/wdl/ResolveComplexVariants.wdl index 1579af637..f712537b6 100644 --- a/wdl/ResolveComplexVariants.wdl +++ b/wdl/ResolveComplexVariants.wdl @@ -1,5 +1,6 @@ version 1.0 +import "ReshardVcf.wdl" as Reshard import "ResolveCpxSv.wdl" as ResolveComplexContig import "TasksMakeCohortVcf.wdl" as MiniTasks @@ -37,6 +38,8 @@ workflow ResolveComplexVariants { RuntimeAttr? runtime_override_breakpoint_overlap_filter RuntimeAttr? runtime_override_subset_inversions RuntimeAttr? runtime_override_concat + RuntimeAttr? runtime_override_concat_bothside_pass + RuntimeAttr? runtime_override_concat_background_fail # overrides for ResolveComplexContig RuntimeAttr? runtime_override_get_se_cutoff @@ -62,6 +65,9 @@ workflow ResolveComplexVariants { RuntimeAttr? runtime_override_preconcat_inv RuntimeAttr? runtime_override_hail_merge_inv RuntimeAttr? runtime_override_fix_header_inv + + # overrides for ReshardVcf + RuntimeAttr? runtime_override_reshard } #Scatter per chromosome @@ -203,6 +209,33 @@ workflow ResolveComplexVariants { } } + call Reshard.ReshardVcf { + input: + vcfs=RenameVariants.renamed_vcf, + contig_list=contig_list, + prefix="~{cohort_name}.reshard_vcf", + sv_base_mini_docker=sv_base_mini_docker, + runtime_override_reshard=runtime_override_reshard + } + + # Due to vcf resharding, these contig-sharded lists are no longer valid + # Here we combine variant list arrays into single genome-wide lists + # This is faster than reshuffling and shouldn't have much performance impact in CleanVcf1a + call MiniTasks.CatUncompressedFiles as ConcatBothsidePass { + input: + shards=UpdateBothsidePass.updated_list, + outfile_name="~{cohort_name}.all.sr_bothside_pass.updated3.txt", + sv_base_mini_docker=sv_base_mini_docker, + runtime_attr_override=runtime_override_concat_bothside_pass + } + call MiniTasks.CatUncompressedFiles as ConcatBackgroundFail { + input: + shards=UpdateBackgroundFail.updated_list, + outfile_name="~{cohort_name}.all.sr_background_fail.updated3.txt", + sv_base_mini_docker=sv_base_mini_docker, + runtime_attr_override=runtime_override_concat_background_fail + } + #Merge resolved vcfs for QC if (merge_vcfs) { call MiniTasks.ConcatVcfs { @@ -218,10 +251,10 @@ workflow ResolveComplexVariants { #Final outputs output { - Array[File] complex_resolve_vcfs = RenameVariants.renamed_vcf - Array[File] complex_resolve_vcf_indexes = RenameVariants.renamed_vcf_index - Array[File] complex_resolve_bothside_pass_lists = UpdateBothsidePass.updated_list - Array[File] complex_resolve_background_fail_lists = UpdateBackgroundFail.updated_list + Array[File] complex_resolve_vcfs = ReshardVcf.resharded_vcfs + Array[File] complex_resolve_vcf_indexes = ReshardVcf.resharded_vcf_indexes + File complex_resolve_bothside_pass_list = ConcatBothsidePass.outfile + File complex_resolve_background_fail_list = ConcatBackgroundFail.outfile Array[File] breakpoint_overlap_dropped_record_vcfs = BreakpointOverlap.dropped_record_vcf Array[File] breakpoint_overlap_dropped_record_vcf_indexes = BreakpointOverlap.dropped_record_vcf_index File? complex_resolve_merged_vcf = ConcatVcfs.concat_vcf