Showing docs for version 3.6-0 | The latest version is 4.1.4.0


AS_BaseQualityRankSumTest

Allele-specific rank Sum Test of REF versus ALT base quality scores

Category Annotation Modules

VCF Field INFO (variant-level)

Type ActiveRegionBasedAnnotation, ReducibleAnnotation, AS_StandardAnnotation

Header definition line
  • INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">

  • Overview

    This variant-level annotation compares the base qualities of the data supporting the reference allele with those supporting each alternate allele. To be clear, it does so separately for each 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 bases supporting the alternate allele have lower quality scores than those supporting the reference allele. Conversely, a positive value indicates that the bases supporting the alternate allele have higher quality scores than those supporting the reference allele. Finding a statistically significant difference either way suggests that the sequencing process may have been biased or affected by an artifact.

    Statistical notes

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

    Caveats

    • Uninformative reads are not used in these calculations.
    • The base quality rank sum test cannot be calculated for sites without a mixture of reads showing both the reference and alternate alleles.

    Related annotations

    • BaseQualityRankSumTest outputs a version of this annotation that includes all alternate alleles in a single calculation.

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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.