diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json index 8f7b64fd5..724abee14 100644 --- a/inputs/values/dockers.json +++ b/inputs/values/dockers.json @@ -12,8 +12,8 @@ "samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2024-10-25-v0.29-beta-5ea22a52", "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2024-10-25-v0.29-beta-5ea22a52", "sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:2024-10-25-v0.29-beta-5ea22a52", - "sv_pipeline_docker": "us-central1-docker.pkg.dev/talkowski-training/kj-development/sv-pipeline:kj-clean-vcf-766acf63d47b59191cfd2362c5acb8311202a904", - "sv_pipeline_qc_docker": "us-central1-docker.pkg.dev/talkowski-training/kj-development/sv-pipeline:kj-clean-vcf-766acf63d47b59191cfd2362c5acb8311202a904", + "sv_pipeline_docker": "us-central1-docker.pkg.dev/talkowski-training/kj-development/sv-pipeline:kj-clean-vcf-d4033870e659b59c96980ba834241a3e68a5865e", + "sv_pipeline_qc_docker": "us-central1-docker.pkg.dev/talkowski-training/kj-development/sv-pipeline:kj-clean-vcf-d4033870e659b59c96980ba834241a3e68a5865e", "wham_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/wham:2024-10-25-v0.29-beta-5ea22a52", "igv_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/igv:mw-xz-fixes-2-b1be6a9", "duphold_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9", @@ -28,5 +28,5 @@ "sv_utils_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-utils:2024-10-25-v0.29-beta-5ea22a52", "gq_recalibrator_docker": "us.gcr.io/broad-dsde-methods/markw/gatk:mw-tb-form-sv-filter-training-data-899360a", "str": "us.gcr.io/broad-dsde-methods/gatk-sv/str:2023-05-23-v0.27.3-beta-e537bdd6", - "denovo": "us-central1-docker.pkg.dev/talkowski-training/kj-development/denovo:kj-clean-vcf-766acf63d47b59191cfd2362c5acb8311202a904" + "denovo": "us-central1-docker.pkg.dev/talkowski-training/kj-development/denovo:kj-clean-vcf-d4033870e659b59c96980ba834241a3e68a5865e" } \ No newline at end of file diff --git a/src/sv-pipeline/04_variant_resolution/scripts/cleanvcf_postprocess.py b/src/sv-pipeline/04_variant_resolution/scripts/cleanvcf_postprocess.py index 16cfeaf04..7efe4d330 100644 --- a/src/sv-pipeline/04_variant_resolution/scripts/cleanvcf_postprocess.py +++ b/src/sv-pipeline/04_variant_resolution/scripts/cleanvcf_postprocess.py @@ -11,12 +11,15 @@ UNR = 'UNR' FILTER_VCF_INFO_LINES = { 'BND_DEPTH', 'BND_MATEID', 'SPLIT_READS', 'PAIRED_END_READS', - 'CLUSTER_MEMBER_IDS', 'MULTIALLELIC', 'UNRESOLVED' + 'CLUSTER_MEMBER_IDS', 'MULTIALLELIC', 'UNRESOLVED', 'VARGQ', + 'EVENT', 'REVISED_EVENT', 'MULTI_CNV' } FILTER_VCF_TEXT_LINES = { 'CIPOS', 'CIEND', 'RMSSTD', 'source', 'bcftools', 'GATKCommandLine', 'fileformat' } +# TODO: Remove INFO fields in advance of script: 'MULTI_CNV', 'VARGQ', 'REVISED_EVENT' + def cleanse_header(header): new_header = pysam.VariantHeader()