From fcc09ede0836325d7d83247afc87c04015f8af4b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 13 Jun 2018 21:05:22 +0200
Subject: [PATCH] Add dbsnp to baserecalibraction
---
gatk.wdl | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 6f52490..78c53b8 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -56,12 +56,17 @@ task BaseRecalibrator {
File inputBamIndex
String recalibrationReportPath
Array[File]+ sequenceGroupInterval
- Array[File]+ knownIndelsSitesVCFs
- Array[File]+ knownIndelsSitesIndices
+ Array[File]? knownIndelsSitesVCFs
+ Array[File]? knownIndelsSitesIndices
+ File? dbsnpVCF
+ File? dbsnpVCFindex
File refDict
File refFasta
File refFastaIndex
+ Array[File]+ knownIndelsSitesVCFsArg = select_all(flatten([knownIndelsSitesVCFs, [dbsnpVCF]]))
+ Array[File]+ knownIndelsSitesIndicesArg = select_all(flatten([knownIndelsSitesIndices, [dbsnpVCFindex]]))
+
Float? memory
Float? memoryMultiplier
@@ -80,7 +85,7 @@ task BaseRecalibrator {
-I ${inputBam} \
--use-original-qualities \
-O ${recalibrationReportPath} \
- --known-sites ${sep=" --known-sites " knownIndelsSitesVCFs} \
+ --known-sites ${sep=" --known-sites " knownIndelsSitesVCFsArg} \
-L ${sep=" -L " sequenceGroupInterval}
}
--
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