@Input(fullName="recal_fileIndex",shortName="",doc="Dependencies on the index of recal_file",required=false,exclusiveOf="",validation="")
privatevarrecal_fileIndex:Seq[File]=Nil
/** The input tranches file describing where to cut the data */
@Input(fullName="tranches_file",shortName="tranchesFile",doc="The input tranches file describing where to cut the data",required=false,exclusiveOf="",validation="")
/** The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value */
@Output(fullName="out",shortName="o",doc="The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value",required=false,exclusiveOf="",validation="")
@Gather(classOf[CatVariantsGatherer])
varout:File=_
/**
* Short name of out
* @return Short name of out
*/
defo=this.out
/**
* Short name of out
* @param value Short name of out
*/
defo_=(value:File){this.out=value}
/** Automatically generated index for out */
@Output(fullName="outIndex",shortName="",doc="Automatically generated index for out",required=false,exclusiveOf="",validation="")
@Gather(enabled=false)
privatevaroutIndex:File=_
/** The truth sensitivity level at which to start filtering */
@Argument(fullName="ts_filter_level",shortName="ts_filter_level",doc="The truth sensitivity level at which to start filtering",required=false,exclusiveOf="",validation="")
varts_filter_level:Option[Double]=None
/** Format string for ts_filter_level */
@Argument(fullName="ts_filter_levelFormat",shortName="",doc="Format string for ts_filter_level",required=false,exclusiveOf="",validation="")
varts_filter_levelFormat:String="%s"
/** The VQSLOD score below which to start filtering */
@Argument(fullName="lodCutoff",shortName="lodCutoff",doc="The VQSLOD score below which to start filtering",required=false,exclusiveOf="",validation="")
varlodCutoff:Option[Double]=None
/** Format string for lodCutoff */
@Argument(fullName="lodCutoffFormat",shortName="",doc="Format string for lodCutoff",required=false,exclusiveOf="",validation="")
varlodCutoffFormat:String="%s"
/** If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file */
@Argument(fullName="ignore_filter",shortName="ignoreFilter",doc="If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file",required=false,exclusiveOf="",validation="")
/** If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file. */
@Argument(fullName="ignore_all_filters",shortName="ignoreAllFilters",doc="If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file.",required=false,exclusiveOf="",validation="")
/** Don't output filtered loci after applying the recalibration */
@Argument(fullName="excludeFiltered",shortName="ef",doc="Don't output filtered loci after applying the recalibration",required=false,exclusiveOf="",validation="")
/** Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously. */
@Argument(fullName="mode",shortName="mode",doc="Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously.",required=false,exclusiveOf="",validation="")
varmode:String=_
/** 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="")
varfilter_reads_with_N_cigar:Boolean=_
/**
* Short name of filter_reads_with_N_cigar
* @return Short name of filter_reads_with_N_cigar
*/
deffilterRNC=this.filter_reads_with_N_cigar
/**
* Short name of filter_reads_with_N_cigar
* @param value Short name of filter_reads_with_N_cigar
/** 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="")
varfilter_mismatching_base_and_quals:Boolean=_
/**
* Short name of filter_mismatching_base_and_quals
* @return Short name of filter_mismatching_base_and_quals
/** 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="")
varfilter_bases_not_stored:Boolean=_
/**
* Short name of filter_bases_not_stored
* @return Short name of filter_bases_not_stored
*/
deffilterNoBases=this.filter_bases_not_stored
/**
* Short name of filter_bases_not_stored
* @param value Short name of filter_bases_not_stored