reference panel and then combine the observed and imputed genotypes to impute SNPs in U1 and U2 in the study sample, but failing to account for the uncertainty in the imputed reference genotypes would probably lead to overconfident and lower-quality inferences. Alternatively, it would be possible to perform separate imputation runs on the SNPs in {U1,T} and the SNPs in {U2,T}, but this approach is neither elegant nor convenient in a large association study.
