diff --git a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl index f79f52fc6..7dd989ca9 100644 --- a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl +++ b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl @@ -22,6 +22,6 @@ "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 b3020d1f0..20db8bce5 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", - 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