jointcaller

Type Members

1. case class AlleleAtLocus(contigName: ContigName, start: Locus, ref: String, alt: String) extends Product with Serializable

   An allele (alt) at a site in the genome.

2. case class Input(index: SampleId, sampleName: SampleName, path: String, tissueType: Input.TissueType.Value, analyte: Input.Analyte.Value) extends readsets.io.Input with Product with Serializable

   An input BAM to the joint variant caller.

3. case class InputCollection(items: PerSample[Input]) extends Product with Serializable

   Convenience container for zero or more Input instances.

4. case class Parameters(maxAllelesPerSite: Int, maxCallsPerSite: Int, anyAlleleMinSupportingReads: Int, anyAlleleMinSupportingPercent: Double, germlineNegativeLog10HeterozygousPrior: Double, germlineNegativeLog10HomozygousAlternatePrior: Double, somaticNegativeLog10VariantPrior: Double, somaticNegativeLog10VariantPriorRna: Double, somaticNegativeLog10VariantPriorWithRnaEvidence: Double, somaticVafFloor: Double, somaticMaxGermlineErrorRatePercent: Double, somaticGenotypePolicy: Parameters.SomaticGenotypePolicy.Value, filterStrandBiasPhred: Double, filterSomaticNormalNonreferencePercent: Double, filterSomaticNormalDepth: Int) extends Product with Serializable

   Model parameters for the joint caller.