org.broadinstitute.hellbender.tools.walkers.annotator

Class OrientationBiasReadCounts

java.lang.Object

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

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

org.broadinstitute.hellbender.tools.walkers.annotator.OrientationBiasReadCounts

All Implemented Interfaces:

Annotation, StandardMutectAnnotation

@DocumentedFeature(groupName="Variant Annotations",
                   groupSummary="Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See https://software.broadinstitute.org/gatk/documentation/article?id=10836",
                   summary="Count of read pairs in the F1R2 and F2R1 configurations supporting REF and ALT alleles (F1R2, F2R1)")
public final class OrientationBiasReadCounts
extends GenotypeAnnotation
implements StandardMutectAnnotation

Count of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate alleles

This is an annotation that gathers information about the read pair configuration for the reads supporting each allele. It can be used along with downstream filtering steps to identify and filter out erroneous variants that occur with higher frequency in one read pair orientation.

References

For more details about the mechanism of oxoG artifact generation, see Discovery and characterization of artefactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. by Costello et al, doi: 10.1093/nar/gks1443

Constructor Summary

Constructors

Constructor and Description
OrientationBiasReadCounts()

Method Summary

Modifier and Type	Method and Description
void	annotate(ReferenceContext refContext, 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.
static void	annotateSingleVariant(htsjdk.variant.variantcontext.VariantContext vc, htsjdk.variant.variantcontext.GenotypeBuilder gb, ReadPileup readPileup, int meanBaseQualityCutoff) Annotate the given variant context with the OxoG read count attributes, directly from the read pileup.
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
protected static boolean	isUsableRead(GATKRead read)

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

OrientationBiasReadCounts

public OrientationBiasReadCounts()

Method Detail

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

annotate

public void annotate(ReferenceContext refContext,
                     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:

refContext - 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

annotateSingleVariant

public static void annotateSingleVariant(htsjdk.variant.variantcontext.VariantContext vc,
                                         htsjdk.variant.variantcontext.GenotypeBuilder gb,
                                         ReadPileup readPileup,
                                         int meanBaseQualityCutoff)

Annotate the given variant context with the OxoG read count attributes, directly from the read pileup. This method may be slow and should be considered EXPERIMENTAL, especially with regard to indels and complex/mixed variants.

Parameters:

vc - variant context for the genotype. Necessary so that we can see all alleles.

gb - genotype builder to put the annotations into.

readPileup - pileup of the reads at this vc. Note that this pileup does not have to match the genotype. In other words, this tool does not check that the pileup was generated from the genotype sample.

isUsableRead

protected static boolean isUsableRead(GATKRead read)