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Multi-sample SNP and indel calling and Outliers

Hi, I was wondering if you have any advice on the effects of including samples of different ancestry in the multiple sample variant calling. We run PCA after calling variants to identify any potential outliers. In case of identifying one, do we have to re-do the SNP and Indel calling step?

Any help most appreciated.

regards,

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Best Answer

  • ebanksebanks Broad Institute ✭✭✭✭
    Accepted Answer

    If you are sure that the sample is truly of different ancestry (and not mis-processed or contaminated) then there are no problems (the outliers won't affect the calls of the cohort in any meaningful way). Even if the outlying samples are mis-processed/contaminated it should be okay, except that I would make sure that there's no systematic problem affecting all samples that only happens to be significant in the outliers.

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    If you are sure that the sample is truly of different ancestry (and not mis-processed or contaminated) then there are no problems (the outliers won't affect the calls of the cohort in any meaningful way). Even if the outlying samples are mis-processed/contaminated it should be okay, except that I would make sure that there's no systematic problem affecting all samples that only happens to be significant in the outliers.

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