diff --git a/gatk.wdl b/gatk.wdl index 3035d805b935767d3a7e80d2565585064527858b..6f5249073e88616d43d9b0dcf29881dfa795d86e 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 }