diff --git a/wdl/CleanVcf5.wdl b/wdl/CleanVcf5.wdl index f9be79029..c7e18592e 100644 --- a/wdl/CleanVcf5.wdl +++ b/wdl/CleanVcf5.wdl @@ -251,7 +251,7 @@ task Polish { bcftools +setGT polished.need_reheader.vcf.gz -- \ -t q \ -n c:'1/1' \ - -i '(INFO/SVTYPE="DEL" | INFO/SVTYPE="DUP") & (FMT/GT~"[2-9]" | FMT/GT~"[1-9][0-9]+") & FMT/RD_CN>3' > polished.need_reheader.regenotyped.vcf + -i '(INFO/SVTYPE="DEL" | INFO/SVTYPE="DUP") & (FMT/GT~"[2-9]" | FMT/GT~"[1-9][0-9]+")' > polished.need_reheader.regenotyped.vcf bgzip polished.need_reheader.regenotyped.vcf