Showing docs for version 3.7-0

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AS_InsertSizeRankSum

Allele specific Rank Sum Test for insert sizes of REF versus ALT reads

Category Annotation Modules

VCF Field INFO (variant-level)

Type ActiveRegionBasedAnnotation, BetaTestingAnnotation, ExperimentalAnnotation, ReducibleAnnotation

Header definition line

INFO=<ID=AS_InsertSizeRankSum,Number=A,Type=Float,Description="Allele-specific Insert Size Rank Sum">

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Overview

This variant-level annotation compares the insert sizes of reads supporting the reference allele with those supporting each alternate allele. To be clear, it does so separately for each 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 are associated with smaller insert sizes than those supporting the reference allele. Conversely, a positive value indicates that reads supporting the alternate allele are associated with larger insert sizes than those supporting the reference allele. Finding a statistically significant difference either way suggests that the sequencing 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 insert sizes (insert sizes of reads supporting REF vs. insert sizes of reads supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

Caveats

• Uninformative reads are not used in these calculations.
• The insert size rank sum test cannot be calculated for sites without a mixture of reads showing both the reference and alternate alleles.
• This is an experimental annotation and as such it is unsupported. Use at your own risk.

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