diff --git a/gatk.wdl b/gatk.wdl index ff17dadcff8286e6e8a6702fa3117f8722a9596a..7e0f5c090735ca729e2548ca69ef03f566bb4848 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} }