Combining subjects genotyped on Illumina versus Affymetrix arrays required an additional QC step to remove SNPs with indeterminate or flipped strand orientation. Specifically, we removed SNPs with ambiguous alleles (i.e., SNPs with A/T or G/C alleles), due to problems with determining strand orientation between the Illumina versus Affymetrix arrays. Then, we used the flip option in PLINK to recode SNPs with an opposing strand orientation relative to the HapMap reference panel. After flipping, we removed a small number of SNPs with misassignment of allele code based on discrepant allele frequencies between the two arrays. The remaining SNPs were used as the input genotypes for imputation.
