/** One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod. */
@Argument(fullName="genotypeFilterExpressionEval",shortName="gfe",doc="One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod.",required=false,exclusiveOf="",validation="")
/** One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod. */
@Argument(fullName="genotypeFilterExpressionComp",shortName="gfc",doc="One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod.",required=false,exclusiveOf="",validation="")
/** File to output the discordant sites and genotypes. */
@Output(fullName="printInterestingSites",shortName="sites",doc="File to output the discordant sites and genotypes.",required=false,exclusiveOf="",validation="")
varprintInterestingSites:Option[File]=None
/** An output file created by the walker. Will overwrite contents if file exists */
@Output(fullName="out",shortName="o",doc="An output file created by the walker. Will overwrite contents if file exists",required=false,exclusiveOf="",validation="")
/** Filter out reads with CIGAR containing the N operator, instead of failing with an error */
@Argument(fullName="filter_reads_with_N_cigar",shortName="filterRNC",doc="Filter out reads with CIGAR containing the N operator, instead of failing with an error",required=false,exclusiveOf="",validation="")
/** Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error */
@Argument(fullName="filter_mismatching_base_and_quals",shortName="filterMBQ",doc="Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error",required=false,exclusiveOf="",validation="")
/** Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error */
@Argument(fullName="filter_bases_not_stored",shortName="filterNoBases",doc="Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error",required=false,exclusiveOf="",validation="")