From 007ef29dd186c78b877f868769a7f2e5478af0f5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Mon, 5 Aug 2019 02:20:05 +0200
Subject: [PATCH] update ModifyStrelka to also add "GT" header
---
somaticseq.wdl | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/somaticseq.wdl b/somaticseq.wdl
index 4a8b860..349c7d2 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -280,9 +280,14 @@ task ModifyStrelka {
}
command {
+ set -e -o pipefail
+
~{installDir}/modify_Strelka.py \
-infile ~{strelkaVCF} \
- -outfile ~{outputVCFName}
+ -outfile "modified_strelka.vcf"
+
+ first_FORMAT_line_num=$(grep -n -m 1 '##FORMAT' "modified_strelka.vcf" | cut -d : -f 1)
+ sed "$first_FORMAT_line_num"'i##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">' "modified_strelka.vcf" > ~{outputVCFName}
}
output {
--
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