filtering included excluding rare (MAF <0.005) and low quality (INFO<0.5) variants, SNPTEST v2.5.225 was used to calculate Hardy-Weinberg Equilibrium (HWE) which yielded 17,461,305 variants. Group (super-population or census race) GWAS filtering was performed using within grouping specific HWE (p-value>10−6) and sample size based MAFs. Instead of using a fixed MAF threshold for each group, the minimum observed minor allele count (MAC) of 40 was used as this minimum is robust for most association analyses performed in GWAS.26
