I performed genome wide assoctiations (linear mixed model, using GENESIS) with about 640'000 SNPs and transformed phenotypic traits of 160 individuals. After correcting for population structure and kinship, all resulting Q-Q plots looked more or less like this:
Does anybody have an idea what could possibly cause deflated p-value distributions in GWAS? Changing the number of PCs and adding different random effects did not substantially improve the model.
Many thanks in advance