clustering model to the reference data, then instructed the software to impute each of the 459 study individuals independently, conditional on the fitted model. Finally, we set IMPUTE v2 to use 40 and 80 conditioning states (k = 40 and k = 80, in separate runs) for phasing updates in both diploid panels and 1,956 reference panel states (2×918+120) for haploid imputation updates in the study sample. As before, we ran the algorithm for 30 MCMC iterations with the first 10 discarded as burn-in, and we specified that the algorithm should choose random conditioning states for phasing updates in the first 3 iterations and informed conditioning states thereafter.
