VQSR filter

Hi,

I have exome sequencing data on 90 samples, and my lab uses the VQSR filter to remove low quality variants. I was wondering if I should also perform a genotype-level filter by DP/GQ post this VQSR filtering step. Is there a protocol that is recommended, or some metrics I can look at to determine if such a step is required?

Thanks,
Shweta

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @shwetaramdas‌,

    We don't provide genotype-level filtering recommendations at this time, but we are working on developing some procedures to refine genotypes. We'll share them on the website as soon as they're ready for public use.

    FYI, the PL values tend to be more useful and informative than GQ for assessing genotypes.

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