Rank sum test for hard-clipped bases on REF versus ALT reads (ClippingRankSum)

Category Variant Annotations

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Overview

Rank Sum Test for hard-clipped bases on REF versus ALT reads

This variant-level annotation tests whether the data supporting the reference allele shows more or less base clipping (hard clips) than those supporting 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 more hard-clipped bases than those supporting the reference allele. Conversely, a positive value indicates that the reads supporting the alternate allele have fewer hard-clipped bases 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 applied to base clips (number of hard-clipped bases on reads supporting REF vs. number of hard-clipped bases on reads supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

Caveat

The clipping rank sum test cannot be calculated for sites without a mixture of reads showing both the reference and alternate alleles.

Really Big Caveat

In AssemblyRegionWalkers the annotation engine receives reads after they have been hard-clipped to fit the assembly region. Thus this annotation should not be used with HaplotypeCaller and Mutect2.

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GATK version 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.