Genotype files were obtained from dbGaP, and updated to release 35 of the probe annotations published by Affymetrix via PLINK43. Probes were filtered out that had a minor allele frequency of <0.01, were missing in >10% of subjects, or did not fit Hardy-Weinberg equilibrium. Subjects were dropped that had an unexpected level of heterozygosity (F>0.05). Finally the HRC-1000G-check-bim.pl script (http://www.well.ox.ac.uk/~wrayner/tools/) was used to perform some final filtering and split data by chromosome. Phasing (via eagle v2.344) and imputation against the HRC r1.1 2016 panel45 (via minimac3) were carried out by the Michigan Imputation Server46.
