Rank sum test for hard-clipped bases on REF versus ALT reads (ClippingRankSum)
Category Variant Annotations
OverviewRank 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.
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.
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.
GATK version 188.8.131.52-SNAPSHOT built at Wed, 4 Mar 2020 13:47:07 -0500.