vcffilter

Type Members

1. case class Args(inputVcf: File = null, outputVcf: File = null, minAvgVariantGQ: Option[Int] = None, invertedOutputVcf: Option[File] = None, minQualScore: Option[Double] = None, minSampleDepth: Int = 1, minTotalDepth: Int = 1, minAlternateDepth: Int = 1, minSamplesPass: Int = 1, mustHaveVariant: List[String] = Nil, mustNotHaveVariant: List[String] = Nil, calledIn: List[String] = Nil, mustHaveGenotype: List[(String, GenotypeType)] = Nil, uniqueVariantInSample: String = null, resToDom: List[Trio] = Nil, trioCompound: List[Trio] = Nil, deNovoTrio: List[Trio] = Nil, trioLossOfHet: List[Trio] = Nil, booleanArgs: BooleanArgs = Args.BooleanArgs(), diffGenotype: List[(String, String)] = Nil, filterHetVarToHomVar: List[(String, String)] = Nil, iDset: Set[String] = Set(), minGenomeQuality: Int = 0, advancedGroups: List[List[String]] = Nil, minCalled: Int = 0, infoArrayMustContain: Map[String, Regex] = Map()) extends Product with Serializable

   

2. class ArgsParser extends AbstractOptParser[Args]