Estimating heritability using GCTA or LDAK in an admixed population

Question

[GabrielMontenegro]

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?

Answer 1

[akang]

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