org.broadinstitute.hellbender.tools.walkers.annotator

Class DepthPerSampleHC

java.lang.Object

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

org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerSampleHC

All Implemented Interfaces:

Annotation, StandardHCAnnotation, StandardMutectAnnotation

@DocumentedFeature(groupName="Variant Annotations",
                   groupSummary="Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See https://software.broadinstitute.org/gatk/documentation/article?id=10836",
                   summary="Depth of informative coverage for each sample (DP)")
public final class DepthPerSampleHC
extends GenotypeAnnotation
implements StandardHCAnnotation, StandardMutectAnnotation

Depth of informative coverage for each sample.

This annotation is similar to the sample-level DP annotation, which counts read depth after general filtering, but with an extra layer of stringency. Its purpose is to provide the count of reads that are actually considered informative by HaplotypeCaller (HC), using pre-read likelihoods that are produced internally by HC.

In this context, an informative read is defined as one that allows the allele it carries to be easily distinguished. In contrast, a read might be considered uninformative if, for example, it only partially overlaps a short tandem repeat and it is not clear whether the read contains the reference allele or an extra repeat.

See the method documentation on using coverage information for important interpretation details.

Caveats

• This annotation can only be generated by HaplotypeCaller (it will not work when called from VariantAnnotator).

Related annotations

• DepthPerAlleleBySample calculates depth of coverage for each allele per sample (AD).
• Coverage gives the filtered depth of coverage for each sample and the unfiltered depth across all samples.

Constructor Summary

Constructors

Constructor and Description
DepthPerSampleHC()

Method Summary

Modifier and Type	Method and Description
void	annotate(ReferenceContext ref, htsjdk.variant.variantcontext.VariantContext vc, htsjdk.variant.variantcontext.Genotype g, htsjdk.variant.variantcontext.GenotypeBuilder gb, AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods) Computes the annotation for the given genotype and the likelihoods per read.
java.util.List<htsjdk.variant.vcf.VCFFormatHeaderLine>	getDescriptions() Return the descriptions used for the VCF FORMAT meta field.
java.util.List<java.lang.String>	getKeyNames() Return the keys

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

DepthPerSampleHC

public DepthPerSampleHC()

Method Detail

annotate

public void annotate(ReferenceContext ref,
                     htsjdk.variant.variantcontext.VariantContext vc,
                     htsjdk.variant.variantcontext.Genotype g,
                     htsjdk.variant.variantcontext.GenotypeBuilder gb,
                     AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods)

Description copied from class: GenotypeAnnotation

Computes the annotation for the given genotype and the likelihoods per read. Expected to modified the passed genotype builder.

Specified by:

annotate in class GenotypeAnnotation

Parameters:

ref - Reference context, may be null

vc - Variant to be annotated. Not null.

g - the genotype to annotate. May be null.

gb - the builder to modify and annotations to. Not null.

likelihoods - matrix of likelihoods indexed by allele and read

getKeyNames

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

Description copied from class: VariantAnnotation

Return the keys

Specified by:

getKeyNames in class VariantAnnotation

getDescriptions

public java.util.List<htsjdk.variant.vcf.VCFFormatHeaderLine> getDescriptions()

Description copied from class: GenotypeAnnotation

Return the descriptions used for the VCF FORMAT meta field. Subclasses must ensure that this list is not null and does not contain null.

Specified by:

getDescriptions in class GenotypeAnnotation