From 6018cb3283b7d5e2a0da183d4761528e7b5092bd Mon Sep 17 00:00:00 2001 From: Megan Shand Date: Tue, 21 May 2024 10:06:01 -0400 Subject: [PATCH 1/5] updates to BGE pipeline from GVS tieout fix string --- .../germline/joint_genotyping/test_inputs/Scientific/bge.json | 3 ++- tasks/broad/JointGenotypingTasks.wdl | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/test_inputs/Scientific/bge.json b/pipelines/broad/dna_seq/germline/joint_genotyping/test_inputs/Scientific/bge.json index 985fedd66f..b74d793cf0 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/test_inputs/Scientific/bge.json +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/test_inputs/Scientific/bge.json @@ -24,7 +24,8 @@ "JointGenotyping.one_thousand_genomes_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz", "JointGenotyping.one_thousand_genomes_resource_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi", - "JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"], + "JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR"], + "JointGenotyping.TrainAndApplyVETS.score_extra_args": " --ignore-all-filters ", "JointGenotyping.use_allele_specific_annotations": false, diff --git a/tasks/broad/JointGenotypingTasks.wdl b/tasks/broad/JointGenotypingTasks.wdl index 65386b0f06..bcea9781a1 100644 --- a/tasks/broad/JointGenotypingTasks.wdl +++ b/tasks/broad/JointGenotypingTasks.wdl @@ -289,7 +289,7 @@ task HardFilterAndMakeSitesOnlyVcf { VariantFiltration \ --filter-expression "ExcessHet > ~{excess_het_threshold}" \ --filter-name ExcessHet \ - ~{"--filter-not-in-mask --mask-name OUTSIDE_OF_TARGETS --mask " + targets_interval_list} \ + ~{"--filter-not-in-mask --mask-description \"Does not overlap the targets interval list.\" --mask-name OUTSIDE_OF_TARGETS --mask " + targets_interval_list} \ -O ~{variant_filtered_vcf_filename} \ -V ~{vcf} From 5d15306ecd456611a8badfdf93cde99d9d2fad21 Mon Sep 17 00:00:00 2001 From: Megan Shand Date: Tue, 10 Sep 2024 11:40:30 -0400 Subject: [PATCH 2/5] changelogs --- .../germline/joint_genotyping/JointGenotyping.changelog.md | 7 +++++++ .../dna_seq/germline/joint_genotyping/JointGenotyping.wdl | 2 +- .../UltimaGenomicsJointGenotyping.changelog.md | 5 +++++ .../UltimaGenomics/UltimaGenomicsJointGenotyping.wdl | 2 +- .../JointGenotypingByChromosomePartOne.changelog.md | 5 +++++ .../by_chromosome/JointGenotypingByChromosomePartOne.wdl | 2 +- .../JointGenotypingByChromosomePartTwo.changelog.md | 5 +++++ .../by_chromosome/JointGenotypingByChromosomePartTwo.wdl | 2 +- 8 files changed, 26 insertions(+), 4 deletions(-) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md index 0e4ae8d8eb..0b9b8c9dba 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md @@ -1,3 +1,10 @@ +# 1.7.1 +2024-09-10 (Date of Last Commit) + +* Update to BGE filtering options in JointCalling. +* If target interval list is provided for filtering, the documentation in the header will be clearer. +* If VETS is enabled, the SCORE annotation will be added to all output variants (even hard filtered sites). + # 1.7.0 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl index 155cacd6ef..bf30156d98 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl @@ -7,7 +7,7 @@ import "https://raw.githubusercontent.com/broadinstitute/gatk/4.5.0.0/scripts/vc # Joint Genotyping for hg38 Whole Genomes and Exomes (has not been tested on hg19) workflow JointGenotyping { - String pipeline_version = "1.7.0" + String pipeline_version = "1.7.1" input { File unpadded_intervals_file diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md index ff9e7a5806..4d9484a2a2 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md @@ -1,3 +1,8 @@ +# 1.2.1 +2024-09-10 (Date of Last Commit) + +* Update to BGE filtering options in JointCalling. This has no effect on this pipeline. + # 1.2.0 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl index bdabd259c4..06722fc971 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl @@ -11,7 +11,7 @@ import "../../../../../../tasks/broad/UltimaGenomicsGermlineFilteringThreshold.w # For choosing a filtering threshold (where on the ROC curve to filter) a sample with truth data is required. workflow UltimaGenomicsJointGenotyping { - String pipeline_version = "1.2.0" + String pipeline_version = "1.2.1" input { File unpadded_intervals_file diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md index 5ea4b2d04e..9e6d983446 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md @@ -1,3 +1,8 @@ +# 1.5.1 +2024-09-10 (Date of Last Commit) + +* Update to BGE filtering options in JointCalling. This has no effect on this pipeline. + # 1.5.0 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl index 9e3f42b1fa..cdcc1b49a5 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl @@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks # Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19) workflow JointGenotypingByChromosomePartOne { - String pipeline_version = "1.5.0" + String pipeline_version = "1.5.1" input { File unpadded_intervals_file diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md index d0d33486a0..74c2d6530e 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md @@ -1,3 +1,8 @@ +# 1.5.1 +2024-09-10 (Date of Last Commit) + +* Update to BGE filtering options in JointCalling. This has no effect on this pipeline. + # 1.5.0 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl index d64214a200..17d23047b0 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl @@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks # Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19) workflow JointGenotypingByChromosomePartTwo { - String pipeline_version = "1.5.0" + String pipeline_version = "1.5.1" input { String callset_name From 6a08d85b0de3f85e67c77081f6420a5a90f180d5 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 10 Sep 2024 15:40:58 +0000 Subject: [PATCH 3/5] Updated pipeline_versions.txt with all pipeline version information --- pipeline_versions.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pipeline_versions.txt b/pipeline_versions.txt index c916cdbb41..8252876a1c 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -14,10 +14,10 @@ BuildCembaReferences 1.0.0 2020-11-15 CEMBA 1.1.7 2024-09-06 GDCWholeGenomeSomaticSingleSample 1.3.3 2024-09-06 UltimaGenomicsWholeGenomeCramOnly 1.0.21 2024-09-06 -JointGenotypingByChromosomePartOne 1.5.0 2024-09-06 -JointGenotypingByChromosomePartTwo 1.5.0 2024-09-06 -UltimaGenomicsJointGenotyping 1.2.0 2024-09-06 -JointGenotyping 1.7.0 2024-09-06 +JointGenotypingByChromosomePartOne 1.5.1 2024-09-10 +JointGenotypingByChromosomePartTwo 1.5.1 2024-09-10 +UltimaGenomicsJointGenotyping 1.2.1 2024-09-10 +JointGenotyping 1.7.1 2024-09-10 ReblockGVCF 2.3.0 2024-09-06 VariantCalling 2.2.2 2024-09-06 WholeGenomeGermlineSingleSample 3.3.0 2024-09-06 From 4e227fdda97719d7ca92bffae023c8f2c521b41e Mon Sep 17 00:00:00 2001 From: ekiernan <55763654+ekiernan@users.noreply.github.com> Date: Mon, 16 Sep 2024 10:20:22 -0400 Subject: [PATCH 4/5] updated JointGenotyping changelog --- .../joint_genotyping/JointGenotyping.changelog.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md index 0b9b8c9dba..590abe52ec 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md @@ -1,9 +1,9 @@ # 1.7.1 2024-09-10 (Date of Last Commit) -* Update to BGE filtering options in JointCalling. -* If target interval list is provided for filtering, the documentation in the header will be clearer. -* If VETS is enabled, the SCORE annotation will be added to all output variants (even hard filtered sites). +* Update to BGE filtering options in JointCalling +* If target interval list is provided for filtering, the documentation in the header will be clearer +* If VETS is enabled, the SCORE annotation will be added to all output variants (even hard filtered sites) # 1.7.0 2024-09-06 (Date of Last Commit) @@ -118,4 +118,4 @@ The `"JointGenotyping.GenotypeGVCFs.allow_old_rms_mapping_quality_annotation_dat Converging WGS and Exome Joint Genotyping into one all-powerful workflow! # 1.0 -Initial release of the ExomeJointGenotyping pipeline \ No newline at end of file +Initial release of the ExomeJointGenotyping pipeline From 1a60e3a478bd6fb80ad003fa35c605921702d9e5 Mon Sep 17 00:00:00 2001 From: meganshand Date: Mon, 16 Sep 2024 10:21:50 -0400 Subject: [PATCH 5/5] Update changelog docs Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com> --- .../UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md | 2 +- .../JointGenotypingByChromosomePartOne.changelog.md | 2 +- .../JointGenotypingByChromosomePartTwo.changelog.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md index 4d9484a2a2..2b18b1a1c5 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md @@ -1,7 +1,7 @@ # 1.2.1 2024-09-10 (Date of Last Commit) -* Update to BGE filtering options in JointCalling. This has no effect on this pipeline. +* Update to BGE filtering options in JointCalling; this has no effect on this pipeline # 1.2.0 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md index 9e6d983446..162fcd033f 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md @@ -1,7 +1,7 @@ # 1.5.1 2024-09-10 (Date of Last Commit) -* Update to BGE filtering options in JointCalling. This has no effect on this pipeline. +* Update to BGE filtering options in JointCalling; this has no effect on this pipeline # 1.5.0 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md index 74c2d6530e..1b4075e674 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md @@ -1,7 +1,7 @@ # 1.5.1 2024-09-10 (Date of Last Commit) -* Update to BGE filtering options in JointCalling. This has no effect on this pipeline. +* Update to BGE filtering options in JointCalling; this has no effect on this pipeline # 1.5.0 2024-09-06 (Date of Last Commit)