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Strand bias estimated by the Symmetric Odds Ratio test

Category Variant Annotations

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation

Header info
  • INFO=

  • 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 StrandOddsRatio annotation is one of several methods that aims to evaluate whether there is strand bias in the data. It is an updated form of the Fisher Strand Test that is better at taking into account large amounts of data in high coverage situations. It is used to determine if there is strand bias between forward and reverse strands for the reference or alternate allele.

    Statistical notes

    Odds Ratios in the 2x2 contingency table below are $$ R = \frac{X[0][0] * X[1][1]}{X[0][1] * X[1][0]} $$ and its inverse:

     + strand - strand
    The sum R + 1/R is used to detect a difference in strand bias for REF and for ALT (the sum makes it symmetric). A high value is indicative of large difference where one entry is very small compared to the others. A scale factor of refRatio/altRatio where $$ refRatio = \frac{max(X[0][0], X[0][1])}{min(X[0][0], X[0][1} $$ and $$ altRatio = \frac{max(X[1][0], X[1][1])}{min(X[1][0], X[1][1]} $$ ensures that the annotation value is large only.

    See the method document on statistical tests for a more detailed explanation of this statistical test.

    Related annotations

    • StrandBiasBySample outputs counts of read depth per allele for each strand orientation.
    • FisherStrand uses Fisher's Exact Test to evaluate strand bias.

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    GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA