Strand bias estimated using Fisher's Exact Test

Category Annotation Modules

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation

Header definition line
  • INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">

  • 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 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.

    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.


    • 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

    • FisherStrand outputs an allele-specific version of this annotation.
    • 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.

    Return to top

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

    GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.