I can't find any description about which one is the effect allele in the documentation...
I could roughly guess from the codes that, at least during the calculation, the folded MAF is used in most of the places (or at least, it's $p(1-p)$ in most places), so the absolute numeric values shouldn't change much. (Please correct me if I'm wrong!) However, this could decide the effect directions and affect harmonization etc....
Your clarification would be greatly appreciated!
I can't find any description about which one is the effect allele in the documentation...$p(1-p)$ in most places), so the absolute numeric values shouldn't change much. (Please correct me if I'm wrong!) However, this could decide the effect directions and affect harmonization etc....
I could roughly guess from the codes that, at least during the calculation, the folded MAF is used in most of the places (or at least, it's
Your clarification would be greatly appreciated!