From 328a1d43d9495b6c431e6a650efe35cd50c82fc9 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 11 Mar 2020 09:22:00 +0100
Subject: [PATCH] add RefConfidence mode
---
gatk.wdl | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/gatk.wdl b/gatk.wdl
index 244a3e2..0ccf519 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -909,6 +909,7 @@ task HaplotypeCaller {
Int? ploidy
String? outputMode
Boolean gvcf = false
+ String emitRefConfidence = if gvcf then "GVCF" else "NONE"
String memory = "12G"
String javaXmx = "4G"
@@ -930,7 +931,7 @@ task HaplotypeCaller {
~{"--pedigree " + pedigree} \
~{"--contamination-fraction-per-sample-file " + contamination} \
~{"--output-mode " + outputMode} \
- ~{true="-ERC GVCF" false="" gvcf}
+ --emit-ref-confidence ~{emitRefConfidence}
}
output {
--
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