feat: added MDM2 and C19MC to cnv amps

genomic-medicine-sweden · Mar 13, 2024 · 5df38b6 · 5df38b6
1 parent 24d01b8
commit 5df38b6
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/config/config.data.hg19.yaml b/config/config.data.hg19.yaml
@@ -30,7 +30,7 @@ arriba_draw_fusion:
   protein_domains: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0/protein_domains_hg19_hs37d5_GRCh37_v2.3.0.gff3"
 
 annotate_cnv:
-  cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes.bed"
+  cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_240307.bed"
   cnv_loh_genes_validated: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_uppsala_genes.bed"
   cnv_loh_genes_all: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes.bed"
 
@@ -57,7 +57,7 @@ call_small_cnv_deletions:
   regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_deletion_genes.tsv"
 
 call_small_cnv_amplifications:
-  regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes.tsv"
+  regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_240307.tsv"
 
 cnvkit_batch:
   normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_36.cnn"
@@ -114,7 +114,7 @@ manta_config_t:
 
 merge_cnv_json:
   annotations:
-    - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes.bed"
+    - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_240307.bed"
     - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes.bed"
 
 mosdepth:

diff --git a/config/config.data.hg38.yaml b/config/config.data.hg38.yaml
@@ -30,7 +30,7 @@ arriba_draw_fusion:
   protein_domains: "{{PROJECT_REF_DATA}}/ref_data/arriba_v2.3.0_hg38/protein_domains_hg38_GRCh38_v2.3.0.gff3"
 
 annotate_cnv:
-  cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38.bed"
+  cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38_240307.bed"
   cnv_loh_genes_validated: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_uppsala_genes_hg38.bed"
   cnv_loh_genes_all: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes_hg38.bed"
 
@@ -57,7 +57,7 @@ call_small_cnv_deletions:
   regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_deletion_genes_hg38.tsv"
 
 call_small_cnv_amplifications:
-  regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_hg38.tsv"
+  regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_hg38_240307.tsv"
 
 cnvkit_batch:
   normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn"
@@ -110,7 +110,7 @@ manta_config_t:
 
 merge_cnv_json:
   annotations:
-    - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38.bed"
+    - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_hg38_240307.bed"
     - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes_hg38.bed"
 
 mosdepth: