Rank sum test of per-read likelihoods of REF versus ALT reads (LikelihoodRankSum)

Category Variant Annotations

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Overview

Rank Sum Test of per-read likelihoods of REF versus ALT reads

This variant-level annotation compares the likelihoods of reads to their best haplotype match, between reads that support the reference allele and those that support 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 likelihoods to their best haplotype match than those supporting the reference allele. Conversely, a positive value indicates that the reads supporting the alternate allele have higher likelihoods to their best haplotype match than those supporting the reference allele. Finding a statistically significant difference either way suggests that the sequencing and/or mapping 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 per-read likelihoods to the best haplotype match (likelihoods of reads supporting REF vs. likelihoods of reads supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

Caveat

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

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GATK version 4.0.8.1 built at 25-41-2019 10:41:16.