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Estimating heritability using GCTA or LDAK in an admixed population

I have GWAS SNP data for an admixed population and I would like to estimate the heritability of my trait under study. I am using LDAK and GCTA to estimate the heritability. However, most studies that I've seen involve homogeneous populations without population structure.

Is there a way to (reliably) estimate heritability taking into account the population structure in my sample?

gcta admixture heritability
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updated by akang akang • written by GabrielMontenegro GabrielMontenegro

1 answer

You can use kinship matrix or GRM which accounts for population structure. For LDAK see –calc-kins-direct and for GCTA see --grm.

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written by akang akang

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