@Output(fullName="out",shortName="o",doc="File to which variants should be written",required=false,exclusiveOf="",validation="")
...
...
@@ -45,39 +45,35 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
/** 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="")
/** One or more classes/groups of annotations to apply to variant calls */
@Argument(fullName="group",shortName="G",doc="One or more classes/groups of annotations to apply to variant calls",required=false,exclusiveOf="",validation="")
vargroup:Seq[String]=Nil
vargroup:List[String]=config("group",default=Nil)
/** One or more specific expressions to apply to variant calls */
@Argument(fullName="expression",shortName="E",doc="One or more specific expressions to apply to variant calls",required=false,exclusiveOf="",validation="")
/** Check for allele concordances when using an external resource VCF file */
@Argument(fullName="resourceAlleleConcordance",shortName="rac",doc="Check for allele concordances when using an external resource VCF file",required=false,exclusiveOf="",validation="")
/** Use all possible annotations (not for the faint of heart) */
@Argument(fullName="useAllAnnotations",shortName="all",doc="Use all possible annotations (not for the faint of heart)",required=false,exclusiveOf="",validation="")
varuseAllAnnotations:Boolean=_
/** List the available annotations and exit */
@Argument(fullName="list",shortName="ls",doc="List the available annotations and exit",required=false,exclusiveOf="",validation="")
/** Add dbSNP ID even if one is already present */
@Argument(fullName="alwaysAppendDbsnpId",shortName="alwaysAppendDbsnpId",doc="Add dbSNP ID even if one is already present",required=false,exclusiveOf="",validation="")
/** Format string for MendelViolationGenotypeQualityThreshold */
@Argument(fullName="MendelViolationGenotypeQualityThresholdFormat",shortName="",doc="Format string for MendelViolationGenotypeQualityThreshold",required=false,exclusiveOf="",validation="")
...
...
@@ -85,15 +81,15 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
/** 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="")
/** 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: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="")
/** One or more stratifications to use when evaluating the data */
@Argument(fullName="select_exps",shortName="select",doc="One or more stratifications to use when evaluating the data",required=false,exclusiveOf="",validation="")
/** Names to use for the list of stratifications (must be a 1-to-1 mapping) */
@Argument(fullName="select_names",shortName="selectName",doc="Names to use for the list of stratifications (must be a 1-to-1 mapping)",required=false,exclusiveOf="",validation="")
/** Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context */
@Argument(fullName="sample",shortName="sn",doc="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context",required=false,exclusiveOf="",validation="")
/** Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets */
@Argument(fullName="known_names",shortName="knownName",doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets",required=false,exclusiveOf="",validation="")
/** One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified) */
@Argument(fullName="stratificationModule",shortName="ST",doc="One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)",required=false,exclusiveOf="",validation="")
/** Do not use the standard stratification modules by default (instead, only those that are specified with the -S option) */
@Argument(fullName="doNotUseAllStandardStratifications",shortName="noST",doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)",required=false,exclusiveOf="",validation="")
/** One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified) */
@Argument(fullName="evalModule",shortName="EV",doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified)",required=false,exclusiveOf="",validation="")
/** Do not use the standard modules by default (instead, only those that are specified with the -EV option) */
@Argument(fullName="doNotUseAllStandardModules",shortName="noEV",doc="Do not use the standard modules by default (instead, only those that are specified with the -EV option)",required=false,exclusiveOf="",validation="")
/** Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50. */
@Argument(fullName="mendelianViolationQualThreshold",shortName="mvq",doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.",required=false,exclusiveOf="",validation="")
/** Format string for mendelianViolationQualThreshold */
@Argument(fullName="mendelianViolationQualThresholdFormat",shortName="",doc="Format string for mendelianViolationQualThreshold",required=false,exclusiveOf="",validation="")
/** Per-sample ploidy (number of chromosomes per sample) */
@Argument(fullName="samplePloidy",shortName="ploidy",doc="Per-sample ploidy (number of chromosomes per sample)",required=false,exclusiveOf="",validation="")
/** If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping */
@Argument(fullName="requireStrictAlleleMatch",shortName="strict",doc="If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping",required=false,exclusiveOf="",validation="")
/** If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes */
@Argument(fullName="keepAC0",shortName="keepAC0",doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes",required=false,exclusiveOf="",validation="")
/** If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes */
@Argument(fullName="numSamples",shortName="numSamples",doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes",required=false,exclusiveOf="",validation="")
varnumSamples:Option[Int]=None
varnumSamples:Option[Int]=config("numSamples")
/** If provided, all -eval tracks will be merged into a single eval track */
@Argument(fullName="mergeEvals",shortName="mergeEvals",doc="If provided, all -eval tracks will be merged into a single eval track",required=false,exclusiveOf="",validation="")
/** File containing tribble-readable features for the IntervalStratificiation */
@Input(fullName="stratIntervals",shortName="stratIntervals",doc="File containing tribble-readable features for the IntervalStratificiation",required=false,exclusiveOf="",validation="")
/** File containing tribble-readable features describing a known list of copy number variants */
@Input(fullName="knownCNVs",shortName="knownCNVs",doc="File containing tribble-readable features describing a known list of copy number variants",required=false,exclusiveOf="",validation="")
varknownCNVs:File=_
varknownCNVs:Option[File]=config("knownCNVs")
/** 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="")
/** Max number of Gaussians for the negative model */
@Argument(fullName="maxNegativeGaussians",shortName="mNG",doc="Max number of Gaussians for the negative model",required=false,exclusiveOf="",validation="")
@Argument(fullName="numKMeans",shortName="nKM",doc="Number of k-means iterations",required=false,exclusiveOf="",validation="")
varnumKMeans:Option[Int]=None
varnumKMeans:Option[Int]=config("numKMeans")
/** Annotation value divergence threshold (number of standard deviations from the means) */
@Argument(fullName="stdThreshold",shortName="std",doc="Annotation value divergence threshold (number of standard deviations from the means) ",required=false,exclusiveOf="",validation="")
/** The shrinkage parameter in the variational Bayes algorithm. */
@Argument(fullName="shrinkage",shortName="shrinkage",doc="The shrinkage parameter in the variational Bayes algorithm.",required=false,exclusiveOf="",validation="")
varshrinkage:Option[Double]=None
varshrinkage:Option[Double]=config("shrinkage")
/** Format string for shrinkage */
@Argument(fullName="shrinkageFormat",shortName="",doc="Format string for shrinkage",required=false,exclusiveOf="",validation="")
/** The dirichlet parameter in the variational Bayes algorithm. */
@Argument(fullName="dirichlet",shortName="dirichlet",doc="The dirichlet parameter in the variational Bayes algorithm.",required=false,exclusiveOf="",validation="")
vardirichlet:Option[Double]=None
vardirichlet:Option[Double]=config("dirichlet")
/** Format string for dirichlet */
@Argument(fullName="dirichletFormat",shortName="",doc="Format string for dirichlet",required=false,exclusiveOf="",validation="")
/** The number of prior counts to use in the variational Bayes algorithm. */
@Argument(fullName="priorCounts",shortName="priorCounts",doc="The number of prior counts to use in the variational Bayes algorithm.",required=false,exclusiveOf="",validation="")
@Argument(fullName="maxNumTrainingData",shortName="maxNumTrainingData",doc="Maximum number of training data",required=false,exclusiveOf="",validation="")
/** LOD score cutoff for selecting bad variants */
@Argument(fullName="badLodCutoff",shortName="badLodCutoff",doc="LOD score cutoff for selecting bad variants",required=false,exclusiveOf="",validation="")
/** Apply logit transform and jitter to MQ values */
@Argument(fullName="MQCapForLogitJitterTransform",shortName="MQCap",doc="Apply logit transform and jitter to MQ values",required=false,exclusiveOf="",validation="")
/** MQ is by default transformed to log[(MQ_cap + epsilon - MQ)/(MQ + epsilon)] to make it more Gaussian-like. Use this flag to not do that. */
@Argument(fullName="no_MQ_logit",shortName="NoMQLogit",doc="MQ is by default transformed to log[(MQ_cap + epsilon - MQ)/(MQ + epsilon)] to make it more Gaussian-like. Use this flag to not do that.",required=false,exclusiveOf="",validation="")
/** Amount of jitter (as a factor to a Normal(0,1) noise) to add to the MQ capped values */
@Argument(fullName="MQ_jitter",shortName="MQJitt",doc="Amount of jitter (as a factor to a Normal(0,1) noise) to add to the MQ capped values",required=false,exclusiveOf="",validation="")
/** 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="")
/** 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="")
/** The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on the optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES! */
@Argument(fullName="target_titv",shortName="titv",doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on the optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!",required=false,exclusiveOf="",validation="")
/** The names of the annotations which should used for calculations */
@Argument(fullName="use_annotation",shortName="an",doc="The names of the annotations which should used for calculations",required=true,exclusiveOf="",validation="")
/** The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent) */
@Argument(fullName="TStranche",shortName="tranche",doc="The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent)",required=false,exclusiveOf="",validation="")
/** If specified, the variant recalibrator will also use variants marked as filtered by the specified filter name in the input VCF file */
@Argument(fullName="ignore_filter",shortName="ignoreFilter",doc="If specified, the variant recalibrator will also use 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="")
/** Used to debug the random number generation inside the VQSR. Do not use. */
@Argument(fullName="replicate",shortName="replicate",doc="Used to debug the random number generation inside the VQSR. Do not use.",required=false,exclusiveOf="",validation="")
varreplicate:Option[Int]=None
varreplicate:Option[Int]=config("replicate")
/** Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation. */
@Argument(fullName="trustAllPolymorphic",shortName="allPoly",doc="Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation.",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="")