individuals from HRC14. To mimic a GWAS, we selected 25 unrelated individuals each from AMD, SardiNIA, BRIDGE Study, and Minnesota Twins and masked all variants except those typed on the Illumina Duo 1M chip (resulting in ~20,000 genotyped variants for chromosome 20). To evaluate imputation accuracy, we estimated the squared Pearson correlation coefficient (r2) between the imputed genotype probabilities and genotype calls from sequence data. We evaluated imputation accuracy at the 227,925 variants that were present in all the respective data sets and had MAF of at least 0.00005 in all contributing studies. For each of the combinations of the four imputation methods and seven reference panels, we recorded the average imputation accuracy, total computational time, and physical memory required to impute 100 GWAS individuals.
