Package org.broadinstitute.hellbender.tools.walkers.annotator

Class MappingQualityRankSumTest

java.lang.Object
org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityRankSumTest
All Implemented Interfaces:
Annotation, InfoFieldAnnotation, StandardAnnotation, VariantAnnotation
@DocumentedFeature(groupName="Variant Annotations", groupSummary="Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See https://software.broadinstitute.org/gatk/documentation/article?id=10836", summary="Rank sum test for mapping qualities of REF versus ALT reads (MQRankSum)") public final class MappingQualityRankSumTest extends RankSumTest implements StandardAnnotation
Rank Sum Test for mapping qualities of REF versus ALT reads

This variant-level annotation compares the mapping qualities of the reads supporting the reference allele with those supporting the alternate allele. The ideal result is a value close to zero, which indicates there is little to no difference. A negative value indicates that the reads supporting the alternate allele have lower mapping quality scores than those supporting the reference allele. Conversely, a positive value indicates that the reads supporting the alternate allele have higher mapping quality scores than those supporting the reference allele.

This annotation can be used to evaluate confidence in a variant call and is a recommended covariate for variant recalibration (VQSR). Finding a statistically significant difference in quality either way suggests that the sequencing and/or mapping process may have been biased or affected by an artifact. In practice, we only filter out low negative values when evaluating variant quality because the idea is to filter out variants for which the quality of the data supporting the alternate allele is comparatively low. The reverse case, where it is the quality of data supporting the reference allele that is lower (resulting in positive ranksum scores), is not really informative for filtering variants.

Statistical notes

The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for mapping qualities (MAPQ of reads supporting REF vs. MAPQ of reads supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

Caveat

The mapping quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.

Related annotations

  • RMSMappingQuality gives an estimation of the overal read mapping quality supporting a variant call.

  • Constructor Details

    • MappingQualityRankSumTest

      public MappingQualityRankSumTest()

  • Method Details

    • getKeyNames

      public List<String> getKeyNames()
      Description copied from interface: VariantAnnotation
      Return the keys
      Specified by:
      getKeyNames in interface VariantAnnotation

    • getElementForRead

      protected OptionalDouble getElementForRead(GATKRead read, htsjdk.variant.variantcontext.VariantContext vc)
      Description copied from class: RankSumTest
      Get the element for the given read at the given reference position
      Specified by:
      getElementForRead in class RankSumTest
      Parameters:
      read - the read
      vc - the variant to be annotated
      Returns:
      an OptionalDouble representing the element to be used in the rank sum test, empty if it should not be used