Specifically, we aim to evaluate the relative performance of several strategies for analyzing the distribution of imputed genotypes in downstream analyses. One summary of these probabilities comes from imputing a “best-guess” genotype for each individual, which corresponds to the marginal mode of the posterior distribution of the unmeasured genotype. This approach ignores the uncertainty in the imputed genotype. When imputation is accurate, the correspondence between the true and imputed genotype is strong and an analysis of the imputed genotypes might result in little loss in power compared with the true genotypes. However, if imputation accuracy is low there may be a weak correlation between the true genotypes and the guesses, which will mask any real association between genotype and phenotype.
