From 3fffcb8e8fe9f4ef259292aaad4036be100d9f65 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 26 Apr 2024 11:14:04 +0200 Subject: [PATCH 1/2] feat: filter noisy genes in umi --- config/filters/config_hard_filter_umi_vep105.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/config/filters/config_hard_filter_umi_vep105.yaml b/config/filters/config_hard_filter_umi_vep105.yaml index e0b4fb64..a66e2b12 100644 --- 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))" From 93c64d30832429175c73367f82f7d8cd26ef5334 Mon Sep 17 00:00:00 2001 From: jonca79 <54137490+jonca79@users.noreply.github.com> Date: Fri, 26 Apr 2024 11:14:59 +0200 Subject: [PATCH 2/2] feat: filter noisy genes in umi --- config/filters/config_soft_filter_umi_vep105.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/config/filters/config_soft_filter_umi_vep105.yaml b/config/filters/config_soft_filter_umi_vep105.yaml index fadf0abe..dda54549 100644 --- 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))"