and subsequently all individuals with a call rate in cases or controls of<0.95 or an autosomal heterozygosity deviation FHET outside the interval [−0.2;0.2] were removed. Individuals where stated sex was not consistent with sex derived from genotypes were flagged. Subsequently QC was conducted at the marker level, keeping markers with call rate ≥0.98, missing difference ≤0.02 between cases and controls, with MAF≥0.01, Hardy-Weinberg equilibrium (HWE) in controls P-value ≥1x10−06 and Hardy-Weinberg equilibrium (HWE) in cases P-value ≥1x10−10 (See https://sites.google.com/a/broadinstitute.org/ricopili/preimputation-qc for further details).
