Package org.broadinstitute.hellbender.tools.walkers.mutect

package org.broadinstitute.hellbender.tools.walkers.mutect

Related Packages

Package	Description
org.broadinstitute.hellbender.tools.walkers
org.broadinstitute.hellbender.tools.walkers.mutect.clustering
org.broadinstitute.hellbender.tools.walkers.mutect.filtering

Class	Description
CreateSomaticPanelOfNormals	Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2.
GatherNormalArtifactData
GetNormalArtifactData	Usage example
M2ArgumentCollection
M2ArgumentCollection.FlowMode	the different flow modes, in terms of their parameters and their values NOTE: a parameter value ending with /o is optional - meaning it will not fail the process if it is not existent on the target parameters collection.
MergeMutectStats	Merge the stats output by scatters of a single Mutect2 job.
Mutect2	Call somatic short mutations via local assembly of haplotypes.
Mutect2Engine	Created by davidben on 9/15/16.
Mutect3DatasetEngine
MutectStats
NormalArtifactRecord
NormalArtifactRecord.NormalArtifactWriter
PerAlleleCollection<X extends Number>	A container for allele to value mapping.
PerAlleleCollection.Type
SomaticGenotypingEngine
SomaticLikelihoodsEngine	Created by David Benjamin on 3/9/17.
SomaticReferenceConfidenceModel
SubsettedLikelihoodMatrix<EVIDENCE extends htsjdk.samtools.util.Locatable,A extends htsjdk.variant.variantcontext.Allele>	Fast wrapper for a LikelihoodMatrix that uses only a subset of alleles.