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LMM GWAS - why are population covariates included?

Hi! I'm new to GWAS and have a theoretical question:

If LMM-based GWAS software (e.g., regenie) can handle sample relatedness (population structure & cryptic relatedness), why are the population covariates included in the analyses?

Thanks for your help :)

lmm gwas population-covariates
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updated by Ram Ram • written by Elizabeth • Elizabeth

Good question - this is something I asked a colleague just yesterday and I believe the answer was that including PCs as covariates helps speed up the estimation of the null GRM used to sample relatedness. But I will double check this and come back..

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written by 4galaxy77 4galaxy77

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