increases AF cutoff to 0.7

Clinical-Genomics · Oct 12, 2021 · 52b10c7 · 52b10c7
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Mitochondrial deletion analysis
 - GATK Haplotypecaller has been turned off in favour of Deepvariant
 - Introduces possibility to store singularity images locally as a .sif file
+- Increased allele frequency cut off for when a variant is filtered out to 0.7
 
 ### Tools
 

diff --git a/definitions/dragen_rd_dna_parameters.yaml b/definitions/dragen_rd_dna_parameters.yaml
@@ -530,7 +530,7 @@ fqf_bcftools_filter_threshold:
   associated_recipe:
     - frequency_filter
   data_type: SCALAR
-  default: 0.40
+  default: 0.70
   type: recipe_argument
 cadd_ar:
   analysis_mode: case

diff --git a/definitions/rd_dna_panel_parameters.yaml b/definitions/rd_dna_panel_parameters.yaml
@@ -831,7 +831,7 @@ fqf_bcftools_filter_threshold:
   associated_recipe:
     - frequency_filter
   data_type: SCALAR
-  default: 0.40
+  default: 0.70
   type: recipe_argument
 cadd_ar:
   analysis_mode: case

diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -1670,7 +1670,7 @@ fqf_bcftools_filter_threshold:
   associated_recipe:
     - frequency_filter
   data_type: SCALAR
-  default: 0.40
+  default: 0.70
   type: recipe_argument
 cadd_ar:
   analysis_mode: case

diff --git a/definitions/rd_dna_vcf_rerun_parameters.yaml b/definitions/rd_dna_vcf_rerun_parameters.yaml
@@ -526,7 +526,7 @@ fqf_bcftools_filter_threshold:
   associated_recipe:
     - frequency_filter
   data_type: SCALAR
-  default: 0.40
+  default: 0.70
   type: recipe_argument
 cadd_ar:
   analysis_mode: case