Current imputation methods are summarized in Supplemental Methods III. Joint imputation using the largest applicable reference panel is expected to perform at least as well as subsetting that reference panel to match the target population (Ahmad et al., 2017; Howie et al., 2012), possibly due to maintaining a larger sample size for phasing. Use of the same reference panel for all cohorts also avoids potential confounding with varying imputation quality. However, it may be necessary to consider imputation quality separately within subsets of individuals even if the samples are jointly imputed since imputation accuracy for a variant may vary widely across individuals of different ancestries.
