Largest contiguous homopolymer run of the variant allele

Category Annotation Modules

VCF Field INFO (variant-level)

Type ExperimentalAnnotation

Header definition line
  • INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">

  • Overview

    Repetitive sequences such as homopolymers are difficult to map to the reference because they are associated with multiple alignment possibilities. The proximity of a long homopolymer to your variant site increases the chance that reads were mapped incorrectly in the surrounding region and lowers confidence in the call. If there is a homopolymer on either side of a site, this annotation outputs the length of its largest run.


    • This can only be computed for bi-allelic sites.
    • The calculation only looks at direct runs of the alternate allele adjacent to this position, which is not a very accurate method.
    • This is an experimental annotation. As such, it is unsupported; we do not make any guarantees that it will work properly, and you use it at your own risk.

    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.