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feat: filter noisy genes #452

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feat: filter noisy genes #452

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60f4c50
feat: filter noisy genes
jonca79 Apr 25, 2024
d49a1cf
feat: filter noisy ge
jonca79 Apr 25, 2024
6f66ba9
feat: filter noisy genes
jonca79 Apr 25, 2024
6e49380
feat: filter noisy genes
jonca79 Apr 25, 2024
ea2f724
feat: filter noisy genes
jonca79 Apr 25, 2024
c85f076
feat: filter noisy genes
jonca79 Apr 25, 2024
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4 changes: 4 additions & 0 deletions config/filters/config_hard_filter_umi_vep105.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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))"
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4 changes: 4 additions & 0 deletions config/filters/config_hard_filter_uppsala_vep105.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
vaf:
description: "Hard filter variants with low vaf (AF lower than 0.01)"
expression: "(FORMAT:AF:0 < 0.01)"
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4 changes: 4 additions & 0 deletions config/filters/config_hard_filter_uppsala_vep107.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
vaf:
description: "Hard filter variants with low vaf (AF lower than 0.01)"
expression: "(FORMAT:AF:0 < 0.01)"
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5 changes: 5 additions & 0 deletions config/filters/config_soft_filter_umi_vep105.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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))"
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5 changes: 5 additions & 0 deletions config/filters/config_soft_filter_uppsala_vep105.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: "Intronic"
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"
vaf:
description: "Soft filter variants with low vaf (AF lower than 0.01)"
expression: "(FORMAT:AF:0 < 0.01)"
Expand Down
5 changes: 5 additions & 0 deletions config/filters/config_soft_filter_uppsala_vep107.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: "Intronic"
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"
vaf:
description: "Soft filter variants with low vaf (AF lower than 0.01)"
expression: "(FORMAT:AF:0 < 0.01)"
Expand Down
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