Updating annotation and gatk code

[arvados-tutorial.git] / cwl / gvcf-to-vcf.cwl

diff --git a/cwl/gvcf-to-vcf.cwl b/cwl/gvcf-to-vcf.cwl
index ecba357fcdd09e4e406c4b3ac7771f53868381f8..dfa3e248da1c19dcd5426cdee894dcd0e8d81f96 100644 (file)
--- a/cwl/gvcf-to-vcf.cwl
+++ b/cwl/gvcf-to-vcf.cwl
@@ -31,6 +31,8 @@ arguments:
   - prefix: "--min-ac"
     valueFrom: "1"
   - $(inputs.gvcf.path)
+  - prefix: "-i"
+    valueFrom: "AVG(GQ)>20"
   - valueFrom: "-Ov"
   - prefix: "-o"
     valueFrom: $(inputs.samplename).vcf