- bedargs := []string{"python2", "-", "--gvcf_type", cmd.gvcfType, infile}
+ bedargs := []string{"python2", "-"}
+ if cmd.gvcfType == "complete_genomics_pass_all" {
+ bedargs = append(bedargs,
+ "--ignore_phrases", "CNV", "INS:ME",
+ "--unreported_is_called",
+ )
+ } else if cmd.gvcfType != "" {
+ bedargs = append(bedargs, "--gvcf_type", cmd.gvcfType)
+ }
+ bedargs = append(bedargs, infile)