@@ -37,11 +38,6 @@ class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with Sc
@Gather(classOf[CatVariantsGatherer])
varout:File=_
/** 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="")
@Input(fullName="known",shortName="known",doc="Input VCF file with known indels",required=false,exclusiveOf="",validation="")
varknown:Seq[File]=Nil
/** Dependencies on any indexes of known */
@Input(fullName="knownIndexes",shortName="",doc="Dependencies on any indexes of known",required=false,exclusiveOf="",validation="")
privatevarknownIndexes:Seq[File]=Nil
varknown:List[File]=config("known",default=Nil)
/** window size for calculating entropy or SNP clusters */
@Argument(fullName="windowSize",shortName="window",doc="window size for calculating entropy or SNP clusters",required=false,exclusiveOf="",validation="")
varwindowSize:Option[Int]=None
varwindowSize:Option[Int]=config("windowSize")
/** fraction of base qualities needing to mismatch for a position to have high entropy */
@Argument(fullName="mismatchFraction",shortName="mismatch",doc="fraction of base qualities needing to mismatch for a position to have high entropy",required=false,exclusiveOf="",validation="")
/** minimum reads at a locus to enable using the entropy calculation */
@Argument(fullName="minReadsAtLocus",shortName="minReads",doc="minimum reads at a locus to enable using the entropy calculation",required=false,exclusiveOf="",validation="")
/** maximum interval size; any intervals larger than this value will be dropped */
@Argument(fullName="maxIntervalSize",shortName="maxInterval",doc="maximum interval size; any intervals larger than this value will be dropped",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="")
@@ -131,11 +132,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
/** VCF file with the truth callset for the reference sample */
@Input(fullName="reference_sample_calls",shortName="referenceCalls",doc="VCF file with the truth callset for the reference sample",required=false,exclusiveOf="",validation="")
varreference_sample_calls:File=_
/** Dependencies on the index of reference_sample_calls */
@Input(fullName="reference_sample_callsIndex",shortName="",doc="Dependencies on the index of reference_sample_calls",required=false,exclusiveOf="",validation="")
@@ -215,11 +212,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
/** 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:File=_
/** Dependencies on the index of alleles */
@Input(fullName="allelesIndex",shortName="",doc="Dependencies on the index of alleles",required=false,exclusiveOf="",validation="")
privatevarallelesIndex:Seq[File]=Nil
varalleles:Option[File]=_
/** 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="")
...
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@@ -251,30 +244,17 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
@Input(fullName="compIndexes",shortName="",doc="Dependencies on any indexes of comp",required=false,exclusiveOf="",validation="")
privatevarcompIndexes:Seq[File]=Nil
/** File to which variants should be written */
@Output(fullName="out",shortName="o",doc="File to which variants should be written",required=false,exclusiveOf="",validation="")
@Gather(classOf[CatVariantsGatherer])
varout:File=_
/** Automatically generated index for out */
@Output(fullName="outIndex",shortName="",doc="Automatically generated index for out",required=false,exclusiveOf="",validation="")
@Gather(enabled=false)
privatevaroutIndex:File=_
/** If provided, only these samples will be emitted into the VCF, regardless of which samples are present in the BAM file */
@Argument(fullName="onlyEmitSamples",shortName="onlyEmitSamples",doc="If provided, only these samples will be emitted into the VCF, regardless of which samples are present in the BAM file",required=false,exclusiveOf="",validation="")
varonlyEmitSamples:Seq[String]=Nil
...
...
@@ -313,16 +293,13 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
@Input(fullName="resourceIndexes",shortName="",doc="Dependencies on any indexes of resource",required=false,exclusiveOf="",validation="")
privatevarresourceIndexes:Seq[File]=Nil
/** File to which variants should be written */
@Output(fullName="out",shortName="o",doc="File to which variants should be written",required=false,exclusiveOf="",validation="")
@Gather(classOf[CatVariantsGatherer])
varout:File=_
/** Automatically generated index for out */
@Output(fullName="outIndex",shortName="",doc="Automatically generated index for out",required=false,exclusiveOf="",validation="")
@Gather(enabled=false)
privatevaroutIndex:File=_
/** One or more specific annotations to apply to variant calls */
@Argument(fullName="annotation",shortName="A",doc="One or more specific annotations to apply to variant calls",required=false,exclusiveOf="",validation="")
varannotation:Seq[String]=Nil
...
...
@@ -138,19 +95,17 @@ class VariantAnnotator(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="")
@Input(fullName="dbsnpIndex",shortName="",doc="Dependencies on the index of dbsnp",required=false,exclusiveOf="",validation="")
privatevardbsnpIndex:Seq[File]=Nil
vardbsnp:Option[File]=None
/** 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="")
vargoldStandard:File=_
/** Dependencies on the index of goldStandard */
@Input(fullName="goldStandardIndex",shortName="",doc="Dependencies on the index of goldStandard",required=false,exclusiveOf="",validation="")
privatevargoldStandardIndex:Seq[File]=Nil
vargoldStandard:Option[File]=None
/** List the available eval modules and exit */
@Argument(fullName="list",shortName="ls",doc="List the available eval modules and exit",required=false,exclusiveOf="",validation="")
@Input(fullName="input",shortName="input",doc="The raw input variants to be recalibrated",required=true,exclusiveOf="",validation="")
varinput:Seq[File]=Nil
/** Dependencies on any indexes of input */
@Input(fullName="inputIndexes",shortName="",doc="Dependencies on any indexes of input",required=false,exclusiveOf="",validation="")
privatevarinputIndexes:Seq[File]=Nil
/** Additional raw input variants to be used in building the model */
@Input(fullName="aggregate",shortName="aggregate",doc="Additional raw input variants to be used in building the model",required=false,exclusiveOf="",validation="")
varaggregate:Seq[File]=Nil
/** Dependencies on any indexes of aggregate */
@Input(fullName="aggregateIndexes",shortName="",doc="Dependencies on any indexes of aggregate",required=false,exclusiveOf="",validation="")
privatevaraggregateIndexes:Seq[File]=Nil
/** A list of sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run) */
@Input(fullName="resource",shortName="resource",doc="A list of sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run)",required=true,exclusiveOf="",validation="")
varresource:Seq[File]=Nil
/** Dependencies on any indexes of resource */
@Input(fullName="resourceIndexes",shortName="",doc="Dependencies on any indexes of resource",required=false,exclusiveOf="",validation="")
privatevarresourceIndexes:Seq[File]=Nil
/** The output recal file used by ApplyRecalibration */
@Output(fullName="recal_file",shortName="recalFile",doc="The output recal file used by ApplyRecalibration",required=true,exclusiveOf="",validation="")
@Gather(classOf[CatVariantsGatherer])
varrecal_file:File=_
/** Automatically generated index for recal_file */
@Output(fullName="recal_fileIndex",shortName="",doc="Automatically generated index for recal_file",required=false,exclusiveOf="",validation="")
@Gather(enabled=false)
privatevarrecal_fileIndex:File=_
/** The output tranches file used by ApplyRecalibration */
@Output(fullName="tranches_file",shortName="tranchesFile",doc="The output tranches file used by ApplyRecalibration",required=true,exclusiveOf="",validation="")