org.broadinstitute.hellbender.tools.walkers.variantutils

Class PosteriorProbabilitiesUtils

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils

public final class PosteriorProbabilitiesUtils
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions A class to wrangle all the various and sundry genotype posterior options, mostly from CalculateGenotypePosteriors

Method Summary

Modifier and Type	Method and Description
protected static java.util.List<double[]>	calculatePosteriorProbs(java.util.List<double[]> genotypeLikelihoods, double[] knownAlleleCountsByAllele, int ploidy, boolean useFlatPriors) Given genotype likelihoods and known allele counts, calculate the posterior probabilities over the genotype states
static htsjdk.variant.variantcontext.VariantContext	calculatePosteriorProbs(htsjdk.variant.variantcontext.VariantContext vc1, java.util.List<htsjdk.variant.variantcontext.VariantContext> resources, int numRefSamplesFromMissingResources, PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions opts) Calculates phred-scaled posterior probabilities for genotypes given the data and allele frequency priors.
static int[]	extractInts(java.lang.Object integerListContainingVCField) Check the formatting on the Object returned by a call to VariantContext::getAttribute() and parse appropriately
static int[]	parsePosteriorsIntoPhredSpace(htsjdk.variant.variantcontext.Genotype genotype)
static double[]	parsePosteriorsIntoProbSpace(htsjdk.variant.variantcontext.Genotype genotype)

Methods inherited from class java.lang.Object

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

Method Detail

calculatePosteriorProbs

public static htsjdk.variant.variantcontext.VariantContext calculatePosteriorProbs(htsjdk.variant.variantcontext.VariantContext vc1,
                                                                                   java.util.List<htsjdk.variant.variantcontext.VariantContext> resources,
                                                                                   int numRefSamplesFromMissingResources,
                                                                                   PosteriorProbabilitiesUtils.PosteriorProbabilitiesOptions opts)

Calculates phred-scaled posterior probabilities for genotypes given the data and allele frequency priors.

Parameters:

vc1 - input variant context

resources - variants to use to calculate genotype priors (should already be checked for matching start position)

numRefSamplesFromMissingResources - the number of reference samples to use for the prior (already accounted for resource missingness)

Returns:

a VariantContext with PLs and PPs in the genotypes and a PG tag for the Phred-scaled prior in the INFO field if

parsePosteriorsIntoPhredSpace

public static int[] parsePosteriorsIntoPhredSpace(htsjdk.variant.variantcontext.Genotype genotype)

parsePosteriorsIntoProbSpace

public static double[] parsePosteriorsIntoProbSpace(htsjdk.variant.variantcontext.Genotype genotype)

calculatePosteriorProbs

protected static java.util.List<double[]> calculatePosteriorProbs(java.util.List<double[]> genotypeLikelihoods,
                                                                  double[] knownAlleleCountsByAllele,
                                                                  int ploidy,
                                                                  boolean useFlatPriors)

Given genotype likelihoods and known allele counts, calculate the posterior probabilities over the genotype states

Parameters:

genotypeLikelihoods - - the genotype likelihoods for the individual

knownAlleleCountsByAllele - - the known allele counts in the population. For AC=2 AN=12 site, this is {10,2}

ploidy - - the ploidy to assume

useFlatPriors - - if true, apply flat priors to likelihoods in order to calculate posterior probabilities

Returns:

- the posterior genotype likelihoods

extractInts

public static int[] extractInts(java.lang.Object integerListContainingVCField)

Check the formatting on the Object returned by a call to VariantContext::getAttribute() and parse appropriately

Parameters:

integerListContainingVCField - - Object returned by a call to VariantContext::getAttribute()

Returns:

- array of ints //Note: if we're working with a integerListContainingVCField that's read directly out of the file it will be a String but if it gets pulled from a VariantContext object built elsewhere in the code it will be an Integer or a List,