From cdd00894febc3401ba4695908da488d9cdcc92c5 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 13 Jun 2018 20:33:18 +0200
Subject: [PATCH] Added dbsnp
---
gatk.wdl | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 3035d80..6f52490 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -193,8 +193,8 @@ task GenotypeGVCFs {
File refFastaIndex
File refDict
- File dbsnpVCF
- File dbsnpVCFindex
+ File? dbsnpVCF
+ File? dbsnpVCFindex
Int? compressionLevel
Float? memory
@@ -215,7 +215,7 @@ task GenotypeGVCFs {
GenotypeGVCFs \
-R ${refFasta} \
-O ${outputPath} \
- -D ${dbsnpVCF} \
+ ${"-D " + dbsnpVCF} \
-G StandardAnnotation \
--only-output-calls-starting-in-intervals \
-new-qual \
@@ -247,6 +247,9 @@ task HaplotypeCallerGvcf {
Int? compressionLevel
String? gatkJar
+ File? dbsnpVCF
+ File? dbsnpVCFindex
+
Float? memory
Float? memoryMultiplier
Int mem = ceil(select_first([memory, 4.0]))
@@ -265,6 +268,7 @@ task HaplotypeCallerGvcf {
-O ${gvcfPath} \
-I ${sep=" -I " inputBams} \
-L ${sep=' -L ' intervalList} \
+ ${"-D " + dbsnpVCF} \
-contamination ${default=0 contamination} \
-ERC GVCF
}
--
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