way. A further increase in speed is obtained by only calculating the marginal copying probabilities at those sites common to the target and reference datasets, and then linearly interpolating these for SNPs in-between those sites that need to be imputed. Imputation was carried out in chunks of approximately 50,000 imputed markers with a 250 kb buffer region and on 5,000 samples per compute job. The combined processing time per sample for the whole genome was approximately 10 min.
