From 817cb4ce407359cc68341f12a677adec43ed9245 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 19 Mar 2018 12:34:14 +0100
Subject: [PATCH] add SplitNCigarReads
---
gatk.wdl | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/gatk.wdl b/gatk.wdl
index 997266c..2a2b2b0 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -194,3 +194,26 @@ task CombineGVCFs {
File output_gvcf_index = output_basename + ".vcf.gz.tbi"
}
}
+
+task SplitNCigarReads {
+ String? preCommand
+
+ File input_bam
+ File ref_fasta
+ String output_bam
+ String gatk_jar
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ java -Xms4G -jar ${gatk_jar} \
+ -I ${input_bam} \
+ -R ${ref_fasta} \
+ -O ${output_bam} # might have to be -o depending on GATK version
+ }
+
+ output {
+ File bam = output_bam
+ File bam_index = output_bam + ".bai"
+ }
+}
--
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