From f377d14ec569f7a44008dae9988f44efd2d55f9f Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 6 Feb 2020 14:31:49 +0100
Subject: [PATCH] add pedigree file
---
gatk.wdl | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/gatk.wdl b/gatk.wdl
index ff17dad..7e0f5c0 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -903,6 +903,7 @@ task HaplotypeCaller {
Float? contamination
File? dbsnpVCF
File? dbsnpVCFIndex
+ File? pedigree
Int? ploidy
Boolean gvcf = false
@@ -922,7 +923,8 @@ task HaplotypeCaller {
~{"--sample-ploidy " + ploidy} \
~{true="-L" false="" defined(intervalList)} ~{sep=' -L ' intervalList} \
~{true="-XL" false="" defined(excludeIntervalList)} ~{sep=' -XL ' excludeIntervalList} \
- ~{"-D" + dbsnpVCF} \
+ ~{"-D " + dbsnpVCF} \
+ ~{"--pedigree " + pedigree} \
~{"--contamination-fraction-per-sample-file " + contamination} \
~{true="-ERC GVCF" false="" gvcf}
}
--
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