@@ -156,7 +156,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
/** The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES */
@Input(fullName="alleles",shortName="alleles",doc="The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES",required=false,exclusiveOf="",validation="")
varalleles:Option[File]=_
varalleles:Option[File]=None
/** Fraction of contamination in sequencing data (for all samples) to aggressively remove */
@Argument(fullName="contamination_fraction_to_filter",shortName="contamination",doc="Fraction of contamination in sequencing data (for all samples) to aggressively remove",required=false,exclusiveOf="",validation="")