For all three studies, care was taken to translate all genotypes to reference genome (b36) forward strand alleles, as subtle errors in genotype strand inference will downwardly bias replication rate estimates. Additional genotypes were imputed with Bimbam (v 0.99) [58], using HAPMAP release 27, build 36 unphased genotypes as reference panels. European American genotypes were imputed with a CEPH reference panel, while African American genotypes were imputed with a combined CEPH and YRI panel. Imputation was run with default Bimbam parameters, and mean imputed genotypes were recorded and used for all downstream analyses.
