From a15663cb60bc462d2d4416a815dc54499f587592 Mon Sep 17 00:00:00 2001 From: jonca79 Date: Thu, 13 Jun 2024 11:07:09 +0200 Subject: [PATCH] feat: rm noisy MUC6 from cnv VAF plot --- config/config.data.hg19.yaml | 2 +- config/config.data.hg38.yaml | 2 +- config/references/design_files.hg19.yaml | 6 +++--- config/references/design_files.hg38.yaml | 6 +++--- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml index bb154743..76093f4b 100644 --- a/config/config.data.hg19.yaml +++ b/config/config.data.hg19.yaml @@ -41,7 +41,7 @@ bcftools_filter_include_region: exon: "{{PROJECT_DESIGN_DATA}}/GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed" bcftools_filter_exclude_region: - blacklist: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnvkit_germline_blacklist_20221221.bed" + blacklist: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnvkit_germline_blacklist_20240613.bed" bcftools_id_snps: snps_bed: "{{PROJECT_DESIGN_DATA}}/GMS560/design/ID_SNPs.bed" diff --git a/config/config.data.hg38.yaml b/config/config.data.hg38.yaml index 3d3546ea..e1c787ec 100644 --- a/config/config.data.hg38.yaml +++ b/config/config.data.hg38.yaml @@ -41,7 +41,7 @@ bcftools_filter_include_region: exon: "{{PROJECT_DESIGN_DATA}}/GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed" bcftools_filter_exclude_region: - blacklist: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnvkit_germline_blacklist_20221221_hg38.bed" + blacklist: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnvkit_germline_blacklist_20240613_hg38.bed" bcftools_id_snps: snps_bed: "{{PROJECT_DESIGN_DATA}}/GMS560/design/ID_SNPs_hg38.bed" diff --git a/config/references/design_files.hg19.yaml b/config/references/design_files.hg19.yaml index dbf6f698..382e1264 100644 --- a/config/references/design_files.hg19.yaml +++ b/config/references/design_files.hg19.yaml @@ -28,10 +28,10 @@ bcftools_filter_exclude_region: blacklist: - checksum: 2eaeb99aa53fc2b7b173c328b6bd1672 - path: GMS560/cnv/cnvkit_germline_blacklist_20221221.bed + checksum: 0e6ad6718e87594732814608a595888b + path: GMS560/cnv/cnvkit_germline_blacklist_20240613.bed type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.1/cnv/cnvkit_germline_blacklist_20221221.bed + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.10.0/cnv/cnvkit_germline_blacklist_20240613.bed bcftools_id_snps: snps_bed: diff --git a/config/references/design_files.hg38.yaml b/config/references/design_files.hg38.yaml index dc2bc0e1..0628a556 100644 --- a/config/references/design_files.hg38.yaml +++ b/config/references/design_files.hg38.yaml @@ -28,10 +28,10 @@ bcftools_filter_exclude_region: blacklist: - checksum: 3911faef7fd360a7960841d2ba4b6054 - path: GMS560/cnv/cnvkit_germline_blacklist_20221221_hg38.bed + checksum: 165084ed176f5b96e98ffc8a7d599f17 + path: GMS560/cnv/cnvkit_germline_blacklist_20240613_hg38.bed type: file - url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.5.0/cnv/cnvkit_germline_blacklist_20221221_hg38.bed + url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.10.0/cnv/cnvkit_germline_blacklist_20240613_hg38.bed bcftools_id_snps: snps_bed: