AS_BaseQualityRankSumTest

Allele-specific rank sum test of REF versus ALT base quality scores (AS_BaseQRankSum)

Category Variant Annotations

Overview

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

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 4.1.4.0 built at Wed, 9 Oct 2019 15:19:59 -0400.