Allele specific Rank Sum Test for mate's mapping qualities of REF versus ALT reads
INFO=<ID=AS_MateMQRankSum,Number=1,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of mate mapping qualities">
This allele specific variant-level annotation compares the mapping qualities of the reads' mates supporting the reference allele with the reads' mates supporting the alternative allele. To be clear, it does so separately for each alternate allele. The Rank Sum Test is using the null hypothesis that the mapping qualities from the reads' mates in the reference allele come from the same distribution as the mapping qualities of the reads' mates in the alternative allele. The alternative hypothesis is that the mapping qualities of the alternative allele reads' mates are stochastically less than the reference allele reads' mates' mapping qualities. Therefore if the resulting Z-score is close to 0 (in other words it follows a standard normal distribution) then there isn't enough evidence to reject the null hypothesis. If you have a more extreme Z-score in the negative direction you know that this variant might have lower quality reads that support the alternative allele (or in this case at least their mates have lower mapping quality).
This annotation can be used to evaluate confidence in a variant call and could be used as a 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.
The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for mapping qualities of the read's mate See the method document on statistical tests for a more detailed explanation of the ranksum test.*
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.