Subtle population stratification not accounted for by the original GWAS could still be an issue, though I don’t expect this would inflate the effects very much. If we had access to raw data we could take into account small correlations between distant variants during finemapping, which would automatically handle assortative mating and stratification.
Subtle population stratification not accounted for by the original GWAS could still be an issue, though I don’t expect this would inflate the effects very much. If we had access to raw data we could take into account small correlations between distant variants during finemapping, which would automatically handle assortative mating and stratification.