Merge pull request #479 from genomic-medicine-sweden/cnv_plot_rm_MUC6

feat: rm noisy MUC6 from cnv VAF plot
genomic-medicine-sweden · Jun 14, 2024 · d2c3287 · d2c3287
2 parents 2d91afc + a15663c
commit d2c3287
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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: