@@ -149,7 +149,7 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with Scat
@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="")
/** 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="")
/** If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping */
@Argument(fullName="dontTrimActiveRegions",shortName="dontTrimActiveRegions",doc="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping",required=false,exclusiveOf="",validation="")
@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="")
/** Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison */
@Input(fullName="goldStandard",shortName="gold",doc="Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison",required=false,exclusiveOf="",validation="")