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HaplotypeScore as an annotation for VariantRecalibrator after UnifiedGenotyper

tommycarstensentommycarstensen United KingdomMember ✭✭✭

The documentation on the HaplotypeScore annotation reads:

HaplotypeCaller does not output this annotation because it already evaluates haplotype segregation internally. This annotation is only informative (and available) for variants called by Unified Genotyper.

The annotation used to be part of the best practices:

http://gatkforums.broadinstitute.org/discussion/15/best-practice-variant-detection-with-the-gatk-v1-x-retired

I will include it in the VQSR model for UG calls from low coverage data. Is this an unwise decision? I guess this is for myself to evaluate. I thought I would ask, in case I have missed something obvious.

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    You're correct that HaplotypeScore would still be Best Practice for UG calls.

    The default values have been optimized for the Broad's pipeline; iirc that's ~30X exomes. If you're working with anything else, consider running a few tests to feel out the range.

Answers

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    I am also slightly puzzled by the different default values for --min_base_quality_score for UG (17) and HC (10). I'm sure these have been tried and tested repeatedly to find the optimal values. I'll stick with the defaults.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    You're correct that HaplotypeScore would still be Best Practice for UG calls.

    The default values have been optimized for the Broad's pipeline; iirc that's ~30X exomes. If you're working with anything else, consider running a few tests to feel out the range.

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