From 689a2f2cfc065bb8e6247c9abb6565698a0c8d9a Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 13 Apr 2018 12:34:52 +0200
Subject: [PATCH] fix SplitNCigarReads
---
gatk.wdl | 1 +
1 file changed, 1 insertion(+)
diff --git a/gatk.wdl b/gatk.wdl
index 3b07d9b..160849a 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -268,6 +268,7 @@ task SplitNCigarReads {
set -e -o pipefail
${preCommand}
java -Xms${mem}G -jar ${gatk_jar} \
+ SplitNCigarReads \
-I ${input_bam} \
-R ${ref_fasta} \
-O ${output_bam} # might have to be -o depending on GATK version \
--
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