From daf19317d6f5aafc4e156910393f8bf02c012199 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 9 Nov 2022 15:27:37 +0100
Subject: [PATCH] remove second breakends in gridss AnnotateSvTypes script
---
gridss.wdl | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/gridss.wdl b/gridss.wdl
index cfe5375..9a09bdd 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -119,9 +119,14 @@ 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)$AF < 0.25, "0/0", "0/1"))
- writeVcf(vcf, out_path, index=~{index})
+ # GRIDSS doesn't supply a GT, simply set it to 0/1
+ geno(vcf)$GT <- "0/1"
+ # Select only one breakend per event (also removes single breakends):
+ # sourceId ends with o or h for paired breakends, the first in the pair
+ # end with o the second with h. Single breakend end with b, these will
+ # also be removed since we can't determine the SVTYPE.
+ gr2 <- gr[grepl(".*o$", gr$sourceId)]
+ writeVcf(vcf[gr2$sourceId], out_path, index=~{index})
EOF
>>>
--
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