Add GT to gridss results in AnnotateSvTypes

gridss.wdl

@@ -119,6 +119,8 @@ task AnnotateSvTypes {
         gr <- breakpointRanges(vcf)
         svtype <- simpleEventType(gr)
         info(vcf[gr$sourceId])$SVTYPE <- svtype
+        # GRIDSS doesn't supply a GT, so we estimate GT based on AF (assuming CN of 2, might be inaccurate)
+        geno(vcf)$GT <- ifelse(geno(vcf)$AF > 0.75, "1/1", ifelse(geno(vcf)$AF < 0.25, "0/0", "0/1"))
         writeVcf(vcf, out_path, index=~{index})
         EOF
     >>>