SNPs were also excluded for deviation from Hardy-Weinberg equilibrium (HWE) in controls at a p < 1 × 10−6, SNP call rate <98% in either cases or controls, a 2% or greater difference in call rate between cases and controls, or minor allele frequency (MAF) < 0.05. After all QC there were 260,474 SNPs available for analysis that captured an estimated 52.2% of common variation at an r2 threshold of 0.8 and 66.3% at a threshold of 0.5 (that better reflects the power of a GWAS29). Total genotyping rates in the final post-QC datasets were 99.8% and 99.9% for autosomal and X SNPs, respectively.
