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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Homopolymeric error sites

How does GATK2 handle the variants called at homopolymeric regions in the genome? Is this feature enabled and used during the variant calling (with UG/HC) or should we do it separately with VariantFilteration. Is there any specific parameter to control this?
Best
Raj

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Raj,
    Currently they are not handled specifically. There is a VariantAnnotator annotation called HRun that looks at homopolymers, but unfortunately it doesn't work very well so we no longer use it in our Best Practices.

  • vsravivsravi Member

    Hi Geraldine, Has there been any update to calling variants near homopolymer runs? From my experience, the most common case of false-positive indel calls from GATK UG are near homopolymer sites. It would be nice to have the option to apply stricter criteria for calling indels near homopolymer sites.

    Thanks,
    Ravi

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Ravi,

    Not internally in the UG, and unfortunately we haven't been able to devote any resources to fixing the HRun annotation. However, the HaplotypeCaller is much better at dealing with this problem. So unless you absolutely have to use the UG (because of ploidy or cohort size) you should try using the HaplotypeCaller. If you do, we'd be interested in hearing back from you on whether you see an improvement in those calls.

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