Untyped SNP genotypes were imputed using HapMap2 as the reference panel. Samples were first phased using Beagle (Browning & Browning, 2009), which takes into account the family structure of the data. Genotypes were then imputed from the phased data using Minimac, which is a computationally efficient version of the MACH program (Y. Li, Willer, Ding, Scheet, & Abecasis, 2010). HapMap2 provided 2,543,887 autosomal SNPs in the r22 reference panel and 64,621 X-chromosome SNPs in the r21 reference panel. Of those SNPs, 501,912 autosomal markers and 11,685 X-chromosome markers had been genotyped for our samples on the Human660W-Quad platform thus leaving 2,041,975 autosomal and 52,936 X SNPs to be imputed. Of those 2,094,911 imputed SNPs, 96.4% had r2 > .5, 90.9% had r2 > .8, 85.2% had r2 > .9 and 77.2% had r2 > .95 in the European-American sample.
