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AS_FisherStrand

Allele-specific strand bias estimated using Fisher's Exact Test *

Category Annotation Modules

VCF Field INFO (variant-level)

Type ActiveRegionBasedAnnotation, ReducibleAnnotation, AS_StandardAnnotation

Header definition line
  • INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">

  • Overview

    Strand bias is a type of sequencing bias in which one DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele vs. the other.

    The AS_FisherStrand annotation is one of several methods that aims to evaluate whether there is strand bias in the data. It uses Fisher's Exact Test to determine if there is strand bias between forward and reverse strands for the reference or alternate allele, and does so separately for each alternate allele.

    The output is a Phred-scaled p-value. The higher the output value, the more likely there is to be bias. More bias is indicative of false positive calls.

    Statistical notes

    See the method document on statistical tests for a more detailed explanation of this application of Fisher's Exact Test.

    Caveats

    • The FisherStrand test may not be calculated for certain complex indel cases or for multi-allelic sites.
    • FisherStrand is best suited for low coverage situations. For testing strand bias in higher coverage situations, see the StrandOddsRatio annotation.

    Related annotations

    • AS_FisherStrand outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • StrandBiasBySample outputs counts of read depth per allele for each strand orientation.
    • StrandOddsRatio is an updated form of FisherStrand that uses a symmetric odds ratio calculation.

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