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Commit 5f6b1817 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixed indexes

parent 217e8ee4
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
View file @ 5f6b1817
......@@ -24,19 +24,19 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
/** SnpEff file from which to get annotations */
@Input(fullName = "snpEffFile", shortName = "snpEffFile", doc = "SnpEff file from which to get annotations", required = false, exclusiveOf = "", validation = "")
var snpEffFile: Option[File] = None
var snpEffFile: Option[File] = config("snpEffFile")
/** dbSNP file */
@Input(fullName = "dbsnp", shortName = "D", doc = "dbSNP file", required = false, exclusiveOf = "", validation = "")
var dbsnp: Option[File] = None
var dbsnp: Option[File] = config("dbsnp")
/** Comparison VCF file */
@Input(fullName = "comp", shortName = "comp", doc = "Comparison VCF file", required = false, exclusiveOf = "", validation = "")
var comp: Seq[File] = Nil
var comp: List[File] = config("comp", default = Nil)
/** External resource VCF file */
@Input(fullName = "resource", shortName = "resource", doc = "External resource VCF file", required = false, exclusiveOf = "", validation = "")
var resource: Seq[File] = Nil
var resource: List[File] = config("resource")
/** File to which variants should be written */
@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 = "")
var annotation: Seq[String] = Nil
var annotation: List[String] = config("annotation", default = Nil, freeVar = false)
/** One or more specific annotations to exclude */
@Argument(fullName = "excludeAnnotation", shortName = "XA", doc = "One or more specific annotations to exclude", required = false, exclusiveOf = "", validation = "")
var excludeAnnotation: Seq[String] = Nil
var excludeAnnotation: List[String] = config("excludeAnnotation", default = Nil)
/** 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 = "")
var group: Seq[String] = Nil
var group: 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 = "")
var expression: Seq[String] = Nil
var expression: List[String] = config("expression", default = Nil)
/** 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 = "")
var resourceAlleleConcordance: Boolean = _
var resourceAlleleConcordance: Boolean = config("resourceAlleleConcordance", default = false)
/** 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 = "")
var useAllAnnotations: Boolean = _
/** List the available annotations and exit */
@Argument(fullName = "list", shortName = "ls", doc = "List the available annotations and exit", required = false, exclusiveOf = "", validation = "")
var list: Boolean = _
var useAllAnnotations: Boolean = config("useAllAnnotations", default = false)
/** 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 = "")
var alwaysAppendDbsnpId: Boolean = _
var alwaysAppendDbsnpId: Boolean = config("alwaysAppendDbsnpId", default = false)
/** GQ threshold for annotating MV ratio */
@Argument(fullName = "MendelViolationGenotypeQualityThreshold", shortName = "mvq", doc = "GQ threshold for annotating MV ratio", required = false, exclusiveOf = "", validation = "")
var MendelViolationGenotypeQualityThreshold: Option[Double] = None
var MendelViolationGenotypeQualityThreshold: Option[Double] = config("MendelViolationGenotypeQualityThreshold")
/** 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 = "")
var filter_reads_with_N_cigar: Boolean = _
var filter_reads_with_N_cigar: Boolean = config("filter_reads_with_N_cigar", default = false)
/** 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 = "")
var filter_mismatching_base_and_quals: Boolean = _
var filter_mismatching_base_and_quals: Boolean = config("filter_mismatching_base_and_quals", default = false)
/** 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 = "")
var filter_bases_not_stored: Boolean = _
var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
override def beforeGraph() {
super.beforeGraph()
......@@ -121,7 +117,6 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
repeat("-E", expression, spaceSeparated = true, escape = true, format = "%s") +
conditional(resourceAlleleConcordance, "-rac", escape = true, format = "%s") +
conditional(useAllAnnotations, "-all", escape = true, format = "%s") +
conditional(list, "-ls", escape = true, format = "%s") +
conditional(alwaysAppendDbsnpId, "-alwaysAppendDbsnpId", escape = true, format = "%s") +
optional("-mvq", MendelViolationGenotypeQualityThreshold, spaceSeparated = true, escape = true, format = MendelViolationGenotypeQualityThresholdFormat) +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
View file @ 5f6b1817
......@@ -64,51 +64,47 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
/** dbSNP file */
@Input(fullName = "dbsnp", shortName = "D", doc = "dbSNP file", required = false, exclusiveOf = "", validation = "")
var dbsnp: Option[File] = None
var dbsnp: Option[File] = config("dbsnp")
/** 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 = "")
var goldStandard: 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 = "")
var list: Boolean = _
var goldStandard: Option[File] = config("goldStandard")
/** 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 = "")
var select_exps: Seq[String] = Nil
var select_exps: List[String] = config("select_exps", default = Nil)
/** 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 = "")
var select_names: Seq[String] = Nil
var select_names: List[String] = config("select_names", default = Nil)
/** 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 = "")
var sample: Seq[String] = Nil
var sample: List[String] = config("sample", default = Nil, freeVar = false
/** 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 = "")
var known_names: Seq[String] = Nil
var known_names: List[String] = config("known_names", default = Nil)
/** 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 = "")
var stratificationModule: Seq[String] = Nil
var stratificationModule: List[String] = config("stratificationModule", default = Nil)
/** 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 = "")
var doNotUseAllStandardStratifications: Boolean = _
var doNotUseAllStandardStratifications: Boolean = config("doNotUseAllStandardStratifications", default = false)
/** 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 = "")
var evalModule: Seq[String] = Nil
var evalModule: List[String] = config("evalModule", default = Nil)
/** 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 = "")
var doNotUseAllStandardModules: Boolean = _
var doNotUseAllStandardModules: Boolean = config("doNotUseAllStandardModules", default = false)
/** Minimum phasing quality */
@Argument(fullName = "minPhaseQuality", shortName = "mpq", doc = "Minimum phasing quality", required = false, exclusiveOf = "", validation = "")
var minPhaseQuality: Option[Double] = None
var minPhaseQuality: Option[Double] = config("minPhaseQuality")
/** Format string for minPhaseQuality */
@Argument(fullName = "minPhaseQualityFormat", shortName = "", doc = "Format string for minPhaseQuality", required = false, exclusiveOf = "", validation = "")
......@@ -116,7 +112,7 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var mendelianViolationQualThreshold: Option[Double] = None
var mendelianViolationQualThreshold: Option[Double] = config("mendelianViolationQualThreshold")
/** Format string for mendelianViolationQualThreshold */
@Argument(fullName = "mendelianViolationQualThresholdFormat", shortName = "", doc = "Format string for mendelianViolationQualThreshold", required = false, exclusiveOf = "", validation = "")
......@@ -124,47 +120,47 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var samplePloidy: Option[Int] = None
var samplePloidy: Option[Int] = config("samplePloidy")
/** Fasta file with ancestral alleles */
@Argument(fullName = "ancestralAlignments", shortName = "aa", doc = "Fasta file with ancestral alleles", required = false, exclusiveOf = "", validation = "")
var ancestralAlignments: File = _
var ancestralAlignments: Option[File] = config("ancestralAlignments")
/** 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 = "")
var requireStrictAlleleMatch: Boolean = _
var requireStrictAlleleMatch: Boolean = config("requireStrictAlleleMatch", default = false)
/** 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 = "")
var keepAC0: Boolean = _
var keepAC0: Boolean = config("keepAC0", default = false)
/** 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 = "")
var numSamples: Option[Int] = None
var numSamples: 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 = "")
var mergeEvals: Boolean = _
var mergeEvals: Boolean = config("mergeEvals", default = false)
/** 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 = "")
var stratIntervals: File = _
var stratIntervals: Option[File] = config("stratIntervals")
/** 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 = "")
var knownCNVs: File = _
var knownCNVs: 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 = "")
var filter_reads_with_N_cigar: Boolean = _
var filter_reads_with_N_cigar: Boolean = config("filter_reads_with_N_cigar", default = false)
/** 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 = "")
var filter_mismatching_base_and_quals: Boolean = _
var filter_mismatching_base_and_quals: Boolean = config("filter_mismatching_base_and_quals", default = false)
/** 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 = "")
var filter_bases_not_stored: Boolean = _
var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
override def freezeFieldValues() {
super.freezeFieldValues()
......@@ -180,7 +176,6 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
optional(TaggedFile.formatCommandLineParameter("-gold", goldStandard), goldStandard, spaceSeparated = true, escape = true, format = "%s") +
conditional(list, "-ls", escape = true, format = "%s") +
repeat("-select", select_exps, spaceSeparated = true, escape = true, format = "%s") +
repeat("-selectName", select_names, spaceSeparated = true, escape = true, format = "%s") +
repeat("-sn", sample, spaceSeparated = true, escape = true, format = "%s") +
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
View file @ 5f6b1817
......@@ -21,23 +21,23 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** Max number of Gaussians for the positive model */
@Argument(fullName = "maxGaussians", shortName = "mG", doc = "Max number of Gaussians for the positive model", required = false, exclusiveOf = "", validation = "")
var maxGaussians: Option[Int] = None
var maxGaussians: Option[Int] = config("maxGaussians")
/** 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 = "")
var maxNegativeGaussians: Option[Int] = None
var maxNegativeGaussians: Option[Int] = config("maxNegativeGaussians")
/** Maximum number of VBEM iterations */
@Argument(fullName = "maxIterations", shortName = "mI", doc = "Maximum number of VBEM iterations", required = false, exclusiveOf = "", validation = "")
var maxIterations: Option[Int] = None
var maxIterations: Option[Int] = config("maxIterations")
/** Number of k-means iterations */
@Argument(fullName = "numKMeans", shortName = "nKM", doc = "Number of k-means iterations", required = false, exclusiveOf = "", validation = "")
var numKMeans: Option[Int] = None
var numKMeans: 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 = "")
var stdThreshold: Option[Double] = None
var stdThreshold: Option[Double] = config("stdThreshold")
/** Format string for stdThreshold */
@Argument(fullName = "stdThresholdFormat", shortName = "", doc = "Format string for stdThreshold", required = false, exclusiveOf = "", validation = "")
......@@ -45,7 +45,7 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var shrinkage: Option[Double] = None
var shrinkage: Option[Double] = config("shrinkage")
/** Format string for shrinkage */
@Argument(fullName = "shrinkageFormat", shortName = "", doc = "Format string for shrinkage", required = false, exclusiveOf = "", validation = "")
......@@ -53,7 +53,7 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var dirichlet: Option[Double] = None
var dirichlet: Option[Double] = config("dirichlet")
/** Format string for dirichlet */
@Argument(fullName = "dirichletFormat", shortName = "", doc = "Format string for dirichlet", required = false, exclusiveOf = "", validation = "")
......@@ -61,7 +61,7 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var priorCounts: Option[Double] = None
var priorCounts: Option[Double] = config("priorCounts")
/** Format string for priorCounts */
@Argument(fullName = "priorCountsFormat", shortName = "", doc = "Format string for priorCounts", required = false, exclusiveOf = "", validation = "")
......@@ -69,15 +69,15 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** Maximum number of training data */
@Argument(fullName = "maxNumTrainingData", shortName = "maxNumTrainingData", doc = "Maximum number of training data", required = false, exclusiveOf = "", validation = "")
var maxNumTrainingData: Option[Int] = None
var maxNumTrainingData: Option[Int] = config("maxNumTrainingData")
/** Minimum number of bad variants */
@Argument(fullName = "minNumBadVariants", shortName = "minNumBad", doc = "Minimum number of bad variants", required = false, exclusiveOf = "", validation = "")
var minNumBadVariants: Option[Int] = None
var minNumBadVariants: Option[Int] = config("minNumBadVariants")
/** LOD score cutoff for selecting bad variants */
@Argument(fullName = "badLodCutoff", shortName = "badLodCutoff", doc = "LOD score cutoff for selecting bad variants", required = false, exclusiveOf = "", validation = "")
var badLodCutoff: Option[Double] = None
var badLodCutoff: Option[Double] = config("badLodCutoff")
/** Format string for badLodCutoff */
@Argument(fullName = "badLodCutoffFormat", shortName = "", doc = "Format string for badLodCutoff", required = false, exclusiveOf = "", validation = "")
......@@ -85,15 +85,15 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var MQCapForLogitJitterTransform: Option[Int] = None
var MQCapForLogitJitterTransform: Option[Int] = config("MQCapForLogitJitterTransform")
/** 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 = "")
var no_MQ_logit: Boolean = _
var no_MQ_logit: Boolean = config("no_MQ_logit", default = false)
/** 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 = "")
var MQ_jitter: Option[Double] = None
var MQ_jitter: Option[Double] = config("MQ_jitter", default = false)
/** Format string for MQ_jitter */
@Argument(fullName = "MQ_jitterFormat", shortName = "", doc = "Format string for MQ_jitter", required = false, exclusiveOf = "", validation = "")
......@@ -105,11 +105,11 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var aggregate: Seq[File] = Nil
var aggregate: List[File] = config("aggregate", default = 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 = "")
var resource: Seq[File] = Nil
var resource: List[File] = config("resource", default = 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 = "")
......@@ -123,7 +123,7 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var target_titv: Option[Double] = None
var target_titv: Option[Double] = config("target_titv")
/** Format string for target_titv */
@Argument(fullName = "target_titvFormat", shortName = "", doc = "Format string for target_titv", required = false, exclusiveOf = "", validation = "")
......@@ -131,15 +131,15 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var use_annotation: Seq[String] = Nil
var use_annotation: List[String] = config("use_annotation", default = Nil)
/** 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 = "")
var TStranche: Seq[Double] = Nil
var TStranche: List[Double] = config("TStranche", default = Nil)
/** 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 = "")
var ignore_filter: Seq[String] = Nil
var ignore_filter: List[String] = config("ignore_filter", default = Nil)
/** 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 = "")
......@@ -152,23 +152,23 @@ class VariantRecalibrator(val root: Configurable) extends CommandLineGATK {
/** 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 = "")
var replicate: Option[Int] = None
var replicate: 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 = "")
var trustAllPolymorphic: Boolean = _
var trustAllPolymorphic: Boolean = config("trustAllPolymorphic", default = false)
/** 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 = "")
var filter_reads_with_N_cigar: Boolean = _
var filter_reads_with_N_cigar: Boolean = config("filter_reads_with_N_cigar", default = false)
/** 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 = "")
var filter_mismatching_base_and_quals: Boolean = _
var filter_mismatching_base_and_quals: Boolean = config("filter_mismatching_base_and_quals", default = false)
/** 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 = "")
var filter_bases_not_stored: Boolean = _
var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
override def freezeFieldValues() {
super.freezeFieldValues()
......
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