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StrandBiasBySample

Number of forward and reverse reads that support REF and ALT alleles

Category Annotation Modules

VCF Field FORMAT (sample genotype-level)

Header definition line
  • FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the 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 StrandBiasBySample annotation produces read counts per allele and per strand that are used by other annotation modules (FisherStrand and StrandOddsRatio) to estimate strand bias using statistical approaches.

    This annotation produces 4 values, corresponding to the number of reads that support the following (in that order):

    • the reference allele on the forward strand
    • the reference allele on the reverse strand
    • the alternate allele on the forward strand
    • the alternate allele on the reverse strand

    Example

    GT:AD:GQ:PL:SB  0/1:53,51:99:1758,0,1835:23,30,33,18

    In this example, the reference allele is supported by 23 forward reads and 30 reverse reads, the alternate allele is supported by 33 forward reads and 18 reverse reads.

    Caveats

    • This annotation can only be generated by HaplotypeCaller (it will not work when called from VariantAnnotator).

    Related annotations

    • FisherStrand uses Fisher's Exact Test to evaluate strand bias.
    • 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.