Merge pull request #457 from genomic-medicine-sweden/umi_noisy_genes

feat: filter noisy genes in umi
genomic-medicine-sweden · Apr 29, 2024 · 6c6d553 · 6c6d553
2 parents a077d64 + 93c64d3
commit 6c6d553
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diff --git a/config/filters/config_hard_filter_umi_vep105.yaml b/config/filters/config_hard_filter_umi_vep105.yaml
@@ -3,6 +3,10 @@ filters:
     description: "Hard filter intronic variants"
     expression: "(exist[intron_variant, VEP:Consequence] and !exist[splice, VEP:Consequence] and VEP:SYMBOL != MET and VEP:SYMBOL != TERT and !exist[COSV[0-9]+, VEP:Existing_variation])"
     soft_filter: "False"
+  noisy_gene:
+    description: "Hard filter variants in noisy genes"
+    expression: "VEP:SYMBOL = MUC6 or VEP:SYMBOL = CDC27"
+    soft_filter: "False"
   artifacts:
     description: "Hard filter variants found in more than 3 normal samples"
     expression: "((INFO:Artifact:0 > 2 and INFO:ArtifactNrSD:0 < 10) or (INFO:Artifact:0 > 2 and INFO:ArtifactNrSD:1 < 10))"

diff --git a/config/filters/config_soft_filter_umi_vep105.yaml b/config/filters/config_soft_filter_umi_vep105.yaml
@@ -4,6 +4,11 @@ filters:
     expression: "(exist[intron_variant, VEP:Consequence] and !exist[splice, VEP:Consequence] and VEP:SYMBOL != MET and VEP:SYMBOL != TERT and !exist[COSV[0-9]+, VEP:Existing_variation])"
     soft_filter_flag: "intron"
     soft_filter: "True"
+  noisy_gene:
+    description: "Hard filter variants in noisy genes"
+    expression: "VEP:SYMBOL = MUC6 or VEP:SYMBOL = CDC27"
+    soft_filter_flag: "noisy_gene"
+    soft_filter: "True"
   artifacts:
     description: "Hard filter variants found in more than 3 normal samples"
     expression: "((INFO:Artifact:0 > 2 and INFO:ArtifactNrSD:0 < 10) or (INFO:Artifact:0 > 2 and INFO:ArtifactNrSD:1 < 10))"