to standard GWAS phasing and imputation on a target sample using a reference panel of size N (as both tasks entail copying shared haplotypes—identified based on data at typed SNPs—from a set of N samples); however, the two tasks also have several important differences and require different algorithms and software (Supplementary Fig. 1). We therefore caution that our in-sample imputation results may not be representative of GWAS imputation performance using an N≈150,000 reference panel.
