org.broadinstitute.hellbender.tools.walkers.annotator

Class ReadPosition

java.lang.Object

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

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

org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosition

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="Median distance of variant starts from ends of reads supporting each allele (MPOS)")
public class ReadPosition
extends PerAlleleAnnotation
implements StandardMutectAnnotation

Median distance of variant starts from ends of reads supporting each alt allele.

The output is an array containing, for each alt allele, the median distance of the variant start from the closest read end over all reads that best match that allele.

For example, for variant context with ref allele A and alt allele C the read position for alt-supporting read GGGGCTT is 2 because the A to C substitution is 2 bases from the right end of the read, which is less than its distance from the left end. For variant context with ref allele AG and alt allele A (deletion) the read position of alt-supporting read ATTTTT is 0. For variant context with ref allele A and alt allele AG (insertion) the read position of alt-supporting read TTTTAG is 1.

The annotation considers only the read's bases themselves and not the position they map to with respect to the reference. For example, suppose a substitution is preceded by 80 matching bases and followed by 10 matching bases, a 10-base deletion, and 10 more matching bases. Its distance from the end of the read is 20 bases, not 30 bases, because the deleted bases belong to the reference, not the read. Similarly soft-clipped bases are counted in the distance.

This annotation is useful for filtering alignment artifacts.

Constructor Summary

Constructors

Constructor and Description
ReadPosition()

Method Summary

Modifier and Type	Method and Description
protected int	aggregate(java.util.List<java.lang.Integer> values)
protected java.lang.String	getDescription()
protected java.util.OptionalInt	getValueForRead(GATKRead read, htsjdk.variant.variantcontext.VariantContext vc)
protected java.lang.String	getVcfKey()

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

annotate, getDescriptions, getKeyNames, includeRefAllele

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

ReadPosition

public ReadPosition()

Method Detail

aggregate

protected int aggregate(java.util.List<java.lang.Integer> values)

Specified by:

aggregate in class PerAlleleAnnotation

getVcfKey

protected java.lang.String getVcfKey()

Specified by:

getVcfKey in class PerAlleleAnnotation

getDescription

protected java.lang.String getDescription()

Specified by:

getDescription in class PerAlleleAnnotation

getValueForRead

protected java.util.OptionalInt getValueForRead(GATKRead read,
                                                htsjdk.variant.variantcontext.VariantContext vc)

Specified by:

getValueForRead in class PerAlleleAnnotation