diff --git a/gatk.wdl b/gatk.wdl index 244a3e2c7f253c008291e6640dfeef7fa6259c5c..0ccf5196027031c3b8433da7f986571cd0ad3997 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -909,6 +909,7 @@ task HaplotypeCaller { Int? ploidy String? outputMode Boolean gvcf = false + String emitRefConfidence = if gvcf then "GVCF" else "NONE" String memory = "12G" String javaXmx = "4G" @@ -930,7 +931,7 @@ task HaplotypeCaller { ~{"--pedigree " + pedigree} \ ~{"--contamination-fraction-per-sample-file " + contamination} \ ~{"--output-mode " + outputMode} \ - ~{true="-ERC GVCF" false="" gvcf} + --emit-ref-confidence ~{emitRefConfidence} } output {