BaseQualityRankSumTest

Rank Sum Test of REF versus ALT base quality scores

Category Annotation Modules

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation

Header definition line
  • INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

  • Overview

    This variant-level annotation compares the base qualities of the data supporting the reference allele with those supporting any 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.

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    GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.