Showing docs for version 3.6-0 | The latest version is 4.1.4.0


LikelihoodRankSumTest

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

Category Annotation Modules

VCF Field INFO (variant-level)

Type ActiveRegionBasedAnnotation

Header definition line
  • INFO=<ID=LikelihoodRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref haplotype likelihoods">

  • Overview

    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.


    Return to top


    See also GATK Documentation Index | Tool Docs Index | Support Forum

    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.