org.broadinstitute.hellbender.tools.walkers.annotator

Class RMSMappingQuality

java.lang.Object

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

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

org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality

All Implemented Interfaces:

ReducibleAnnotation, 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="Root mean square of the mapping quality of reads across all samples (MQ)")
public final class RMSMappingQuality
extends InfoFieldAnnotation
implements StandardAnnotation, ReducibleAnnotation

Root Mean Square of the mapping quality of reads across all samples.

This annotation provides an estimation of the overall mapping quality of reads supporting a variant call, averaged over all samples in a cohort.

Statistical notes

The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.

Related annotations

• MappingQualityRankSumTest compares the mapping quality of reads supporting the REF and ALT alleles.

Constructor Summary

Constructors

Constructor and Description
RMSMappingQuality()

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.Map<java.lang.String,java.lang.Object>	annotateRawData(ReferenceContext ref, htsjdk.variant.variantcontext.VariantContext vc, ReadLikelihoods<htsjdk.variant.variantcontext.Allele> likelihoods) Generate the raw data necessary to calculate the annotation.
void	calculateRawData(htsjdk.variant.variantcontext.VariantContext vc, ReadLikelihoods<htsjdk.variant.variantcontext.Allele> likelihoods, ReducibleAnnotationData rawAnnotations)
void	combineAttributeMap(ReducibleAnnotationData<java.lang.Double> toAdd, ReducibleAnnotationData<java.lang.Double> combined)
java.util.Map<java.lang.String,java.lang.Object>	combineRawData(java.util.List<htsjdk.variant.variantcontext.Allele> vcAlleles, java.util.List<ReducibleAnnotationData<?>> annotationList) Combine raw data, typically during the merging of raw data contained in multiple gVCFs as in CombineGVCFs and the preliminary merge for GenotypeGVCFs
java.util.Map<java.lang.String,java.lang.Object>	finalizeRawData(htsjdk.variant.variantcontext.VariantContext vc, htsjdk.variant.variantcontext.VariantContext originalVC) Calculate the final annotation value from the raw data which was generated by either annotateRawData or calculateRawData
htsjdk.variant.variantcontext.VariantContext	finalizeRawMQ(htsjdk.variant.variantcontext.VariantContext vc) converts GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY into VCFConstants.RMS_MAPPING_QUALITY_KEY annotation if present
java.util.List<htsjdk.variant.vcf.VCFInfoHeaderLine>	getDescriptions() Returns the descriptions used for the VCF INFO meta field.
static RMSMappingQuality	getInstance()
java.util.List<java.lang.String>	getKeyNames() Return the keys
java.util.List<htsjdk.variant.vcf.VCFInfoHeaderLine>	getRawDescriptions() Returns the descriptions used for the VCF INFO meta field corresponding to the annotations raw key.
java.lang.String	getRawKeyName()
java.lang.String	makeFinalizedAnnotationString(int numOfReads, java.util.Map<htsjdk.variant.variantcontext.Allele,java.lang.Double> perAlleleData)
java.lang.String	makeRawAnnotationString(java.util.List<htsjdk.variant.variantcontext.Allele> vcAlleles, java.util.Map<htsjdk.variant.variantcontext.Allele,java.lang.Number> perAlleleData)
protected void	parseRawDataString(ReducibleAnnotationData<java.lang.Number> myData)

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

RMSMappingQuality

public RMSMappingQuality()

Method Detail

getRawKeyName

public java.lang.String getRawKeyName()

Specified by:

getRawKeyName in interface ReducibleAnnotation

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.VCFInfoHeaderLine> getDescriptions()

Description copied from class: InfoFieldAnnotation

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

Overrides:

getDescriptions in class InfoFieldAnnotation

getRawDescriptions

public java.util.List<htsjdk.variant.vcf.VCFInfoHeaderLine> getRawDescriptions()

Description copied from interface: ReducibleAnnotation

Returns the descriptions used for the VCF INFO meta field corresponding to the annotations raw key.

Specified by:

getRawDescriptions in interface ReducibleAnnotation

Returns:

A list of VCFInfoHeaderLines corresponding to the raw keys added by this annotaiton

annotateRawData

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

Generate the raw data necessary to calculate the annotation. Raw data is the final endpoint for gVCFs.

Specified by:

annotateRawData in interface ReducibleAnnotation

Parameters:

ref - the reference context for this annotation

vc - the variant context to annotate

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

combineRawData

public java.util.Map<java.lang.String,java.lang.Object> combineRawData(java.util.List<htsjdk.variant.variantcontext.Allele> vcAlleles,
                                                                       java.util.List<ReducibleAnnotationData<?>> annotationList)

Description copied from interface: ReducibleAnnotation

Combine raw data, typically during the merging of raw data contained in multiple gVCFs as in CombineGVCFs and the preliminary merge for GenotypeGVCFs

Specified by:

combineRawData in interface ReducibleAnnotation

Parameters:

vcAlleles - The merged allele list across all variants being combined/merged

annotationList - The raw data for all the variants being combined/merged

Returns:

A key, Object map containing the annotations generated by this combine operation

makeRawAnnotationString

public java.lang.String makeRawAnnotationString(java.util.List<htsjdk.variant.variantcontext.Allele> vcAlleles,
                                                java.util.Map<htsjdk.variant.variantcontext.Allele,java.lang.Number> perAlleleData)

finalizeRawData

public java.util.Map<java.lang.String,java.lang.Object> finalizeRawData(htsjdk.variant.variantcontext.VariantContext vc,
                                                                        htsjdk.variant.variantcontext.VariantContext originalVC)

Description copied from interface: ReducibleAnnotation

Calculate the final annotation value from the raw data which was generated by either annotateRawData or calculateRawData

Specified by:

finalizeRawData in interface ReducibleAnnotation

Parameters:

vc - -- contains the final set of alleles, possibly subset by GenotypeGVCFs

originalVC - -- used to get all the alleles for all gVCFs

Returns:

A key, Object map containing the finalized annotations generated by this operation to be added to the code

makeFinalizedAnnotationString

public java.lang.String makeFinalizedAnnotationString(int numOfReads,
                                                      java.util.Map<htsjdk.variant.variantcontext.Allele,java.lang.Double> perAlleleData)

combineAttributeMap

public void combineAttributeMap(ReducibleAnnotationData<java.lang.Double> toAdd,
                                ReducibleAnnotationData<java.lang.Double> combined)

calculateRawData

public void calculateRawData(htsjdk.variant.variantcontext.VariantContext vc,
                             ReadLikelihoods<htsjdk.variant.variantcontext.Allele> likelihoods,
                             ReducibleAnnotationData rawAnnotations)

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

finalizeRawMQ

public htsjdk.variant.variantcontext.VariantContext finalizeRawMQ(htsjdk.variant.variantcontext.VariantContext vc)

converts GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY into VCFConstants.RMS_MAPPING_QUALITY_KEY annotation if present

Parameters:

vc - which potentially contains rawMQ

Returns:

if vc contained GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY it will be replaced with VCFConstants.RMS_MAPPING_QUALITY_KEY otherwise return the original vc

parseRawDataString

protected void parseRawDataString(ReducibleAnnotationData<java.lang.Number> myData)

getInstance

public static RMSMappingQuality getInstance()