org.broadinstitute.hellbender.tools.walkers.annotator

Class InbreedingCoeff

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff

All Implemented Interfaces:

Annotation, StandardAnnotation

@DocumentedFeature(groupName="Variant Annotations",
                   groupSummary="Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See https://software.broadinstitute.org/gatk/documentation/article?id=10836",
                   summary="Likelihood-based test for the consanguinity among samples (InbreedingCoeff)")
public final class InbreedingCoeff
extends PedigreeAnnotation
implements StandardAnnotation

Likelihood-based test for the consanguinuity among samples

This annotation estimates whether there is evidence of consanguinuity in a population. The higher the score, the higher the chance that some samples are related. If samples are known to be related, a pedigree file can be provided so that the calculation is only performed on founders and offspring are excluded.

Statistical notes

The calculation is a continuous generalization of the Hardy-Weinberg test for disequilibrium that works well with limited coverage per sample. The output is a Phred-scaled p-value derived from running the HW test for disequilibrium with PL values. See the method document on statistical tests for a more detailed explanation of this statistical test.

Caveats

• The Inbreeding Coefficient annotation can only be calculated for cohorts containing at least 10 founder samples.
• The Inbreeding Coefficient annotation can only be calculated for diploid samples.

Related annotations

ExcessHet also describes the heterozygosity of the called samples, giving a probability of excess heterozygosity being observed

Constructor Summary

Constructors

Constructor and Description
InbreedingCoeff()
InbreedingCoeff(java.io.File pedigreeFile)
InbreedingCoeff(java.util.Set<java.lang.String> founderIds)

Method Summary

Modifier and Type	Method and Description
java.util.Map<java.lang.String,java.lang.Object>	annotate(ReferenceContext ref, htsjdk.variant.variantcontext.VariantContext vc, ReadLikelihoods<htsjdk.variant.variantcontext.Allele> likelihoods) Computes the annotation for the given variant and the likelihoods per read.
java.util.List<java.lang.String>	getKeyNames() Return the keys

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation

getFounderGenotypes, setFounderIds, setPedigreeFile

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation

getDescriptions

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation

toString

Methods inherited from class java.lang.Object

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

Constructor Detail

InbreedingCoeff

public InbreedingCoeff()

InbreedingCoeff

public InbreedingCoeff(java.util.Set<java.lang.String> founderIds)

InbreedingCoeff

public InbreedingCoeff(java.io.File pedigreeFile)

Method Detail

annotate

public java.util.Map<java.lang.String,java.lang.Object> annotate(ReferenceContext ref,
                                                                 htsjdk.variant.variantcontext.VariantContext vc,
                                                                 ReadLikelihoods<htsjdk.variant.variantcontext.Allele> likelihoods)

Description copied from class: InfoFieldAnnotation

Computes the annotation for the given variant and the likelihoods per read. Returns a map from annotation keys to values (may be empty if no annotation is to be added).

Specified by:

annotate in class InfoFieldAnnotation

Parameters:

ref - Reference context, may be null

vc - Variant to be annotated. Not null.

likelihoods - likelihoods indexed by sample, allele, and read within sample

getKeyNames

public java.util.List<java.lang.String> getKeyNames()

Description copied from class: VariantAnnotation

Return the keys

Specified by:

getKeyNames in class VariantAnnotation