From 0f3cb30df3276150f6b168ebfc43ed596d9f140b Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 4 Jul 2022 16:10:59 +0200
Subject: [PATCH] Add GT to gridss results in AnnotateSvTypes
---
gridss.wdl | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gridss.wdl b/gridss.wdl
index 38daa02..35e41d2 100644
--- a/gridss.wdl
+++ b/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
>>>
--
GitLab