variants

Type Members

1. case class Allele(refBases: Seq[Byte], altBases: Seq[Byte]) extends Ordered[Allele] with Product with Serializable

2. case class AlleleEvidence(likelihood: Double, readDepth: Int, alleleReadDepth: Int, forwardDepth: Int, alleleForwardDepth: Int, meanMappingQuality: Double, medianMappingQuality: Double, meanBaseQuality: Double, medianBaseQuality: Double, medianMismatchesPerRead: Double) extends Product with Serializable

   Sample specific pileup and read statistics in support of a given variant

3. class AlleleSerializer extends Serializer[Allele]

4. case class CalledAllele(sampleName: SampleName, contigName: ContigName, start: Locus, allele: Allele, evidence: AlleleEvidence, rsID: Option[Int] = scala.None, length: NumLoci = 1) extends ReferenceVariant with Product with Serializable

   A variant that exists in the sample; includes supporting read statistics

5. case class CalledSomaticAllele(sampleName: SampleName, contigName: ContigName, start: Locus, allele: Allele, somaticLogOdds: Double, tumorVariantEvidence: AlleleEvidence, normalReferenceEvidence: AlleleEvidence, rsID: Option[Int] = scala.None, length: NumLoci = 1) extends ReferenceVariant with Product with Serializable

   A variant that exists in a tumor sample, but not in the normal sample; includes supporting read statistics from both samples

6. case class Genotype(alleleMixture: Map[Allele, Double]) extends Product with Serializable

   A Genotype is a map of alleles to their allele frequency

7. trait GenotypeOutputArgs extends Args4jBase with ParquetArgs

   Arguments for writing output genotypes.

8. trait GenotypeOutputCaller[ArgsT <: Args with GenotypeOutputArgs, V <: ReferenceVariant] extends SparkCommand[ArgsT]

   Caller-interface that writes computed variants to disk according to a GenotypeOutputArgs.

9. trait HasAlleleSerializer extends AnyRef

10. trait ReferenceVariant extends ReferenceRegion

    Base properties of a genomic change in a sequence sample from a reference genome