org.broadinstitute.hellbender.tools.walkers.mutect

Class GermlineProbabilityCalculator

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.mutect.GermlineProbabilityCalculator

public class GermlineProbabilityCalculator
extends java.lang.Object

Created by David Benjamin on 5/4/17.

Constructor Summary

Constructors

Constructor and Description
GermlineProbabilityCalculator()

Method Summary

Modifier and Type	Method and Description
static double[]	calculateGermlineProbabilities(double[] populationAlleleFrequencies, double[] log10OddsOfGermlineHetVsSomatic, double[] log10OddsOfGermlineHomAltVsSomatic, java.util.Optional<double[]> normalLog10Odds, double log10PriorProbOfSomaticEvent)
static java.util.Map<java.lang.String,java.lang.Object>	getPopulationAFAnnotation(java.util.List<htsjdk.variant.variantcontext.VariantContext> germlineResourceVariants, java.util.List<htsjdk.variant.variantcontext.Allele> altAlleles, double afOfAllelesNotInGermlineResource)
static double	log10PosteriorProbabilityOfGermlineVariant(double normalLog10Odds, double log10OddsOfGermlineHetVsSomatic, double log10OddsOfGermlineHomAltVsSomatic, double populationAlleleFrequency, double log10PriorProbOfSomaticEvent)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GermlineProbabilityCalculator

public GermlineProbabilityCalculator()

Method Detail

getPopulationAFAnnotation

public static java.util.Map<java.lang.String,java.lang.Object> getPopulationAFAnnotation(java.util.List<htsjdk.variant.variantcontext.VariantContext> germlineResourceVariants,
                                                                                         java.util.List<htsjdk.variant.variantcontext.Allele> altAlleles,
                                                                                         double afOfAllelesNotInGermlineResource)

calculateGermlineProbabilities

public static double[] calculateGermlineProbabilities(double[] populationAlleleFrequencies,
                                                      double[] log10OddsOfGermlineHetVsSomatic,
                                                      double[] log10OddsOfGermlineHomAltVsSomatic,
                                                      java.util.Optional<double[]> normalLog10Odds,
                                                      double log10PriorProbOfSomaticEvent)

log10PosteriorProbabilityOfGermlineVariant

public static double log10PosteriorProbabilityOfGermlineVariant(double normalLog10Odds,
                                                                double log10OddsOfGermlineHetVsSomatic,
                                                                double log10OddsOfGermlineHomAltVsSomatic,
                                                                double populationAlleleFrequency,
                                                                double log10PriorProbOfSomaticEvent)

Parameters:

normalLog10Odds - the log10 likelihood ratio between 1) allele being present in normal (as a diploid het or hom var and not as an artifact) and 2) not being present. Since likelihoods are meaningful only up to an arbitrary constant factor, we may interpret this as the log10 likelihood that the allele exists in the normal provided that the likelihood that it does not exist is log10(1) = 0.

log10OddsOfGermlineHetVsSomatic - the log10 likelihood ratio between 1) allele being present in tumor as a germline het (using information about the minor allele fraction) and 2) being present, as a somatic variant as calculated by the SomaticGenotypingEngine

populationAlleleFrequency - frequency of this allele in the population -- serves as a prior for germline allele

log10PriorProbOfSomaticEvent - the log10 prior probability for this allele to arise de novo in the tumor

Returns:

log10 of the posterior probability that this allele exists in the normal sample