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.

The raw data format for this annotation consists of a list of two entries: the sum of the squared mapping qualities and the number of reads across variant (not homRef) genotypes

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.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	allowOlderRawKeyValues
static java.lang.String	RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT

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, AlleleLikelihoods<GATKRead,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, AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods) Generate the raw data necessary to calculate the annotation.
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_MAPPING_QUALITY_WITH_DEPTH_KEY into VCFConstants.RMS_MAPPING_QUALITY_KEY annotation if present NOTE: this is currently only used by HaplotypeCaller in VCF mode and GnarlyGenotyper
static java.lang.String	getDeprecatedRawKeyName()
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.lang.String	getPrimaryRawKey() Get the string that's used to combine data for this annotation
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.util.List<java.lang.String>	getSecondaryRawKeys() Get additional raw key strings that are not the primary key
boolean	hasSecondaryRawKeys()

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

Methods inherited from interface org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation

getRawKeyNames

Field Detail

RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT

public static final java.lang.String RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT

See Also:

Constant Field Values

allowOlderRawKeyValues

@Argument(fullName="allow-old-rms-mapping-quality-annotation-data",
          doc="Override to allow old RMSMappingQuality annotated VCFs to function",
          optional=true)
public boolean allowOlderRawKeyValues

Constructor Detail

RMSMappingQuality

public RMSMappingQuality()

Method Detail

getPrimaryRawKey

public java.lang.String getPrimaryRawKey()

Description copied from interface: ReducibleAnnotation

Get the string that's used to combine data for this annotation

Specified by:

getPrimaryRawKey in interface ReducibleAnnotation

Returns:

never null

hasSecondaryRawKeys

public boolean hasSecondaryRawKeys()

Specified by:

hasSecondaryRawKeys in interface ReducibleAnnotation

Returns:

true if annotation has secondary raw keys

getSecondaryRawKeys

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

Get additional raw key strings that are not the primary key

Specified by:

getSecondaryRawKeys in interface ReducibleAnnotation

Returns:

may be null

getDeprecatedRawKeyName

public static java.lang.String getDeprecatedRawKeyName()

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,
                                                                        AlleleLikelihoods<GATKRead,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

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

annotate

public java.util.Map<java.lang.String,java.lang.Object> annotate(ReferenceContext ref,
                                                                 htsjdk.variant.variantcontext.VariantContext vc,
                                                                 AlleleLikelihoods<GATKRead,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_MAPPING_QUALITY_WITH_DEPTH_KEY into VCFConstants.RMS_MAPPING_QUALITY_KEY annotation if present NOTE: this is currently only used by HaplotypeCaller in VCF mode and GnarlyGenotyper

Parameters:

vc - which potentially contains rawMQ

Returns:

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

getInstance

public static RMSMappingQuality getInstance()