haplotypes (up to 500 per individual, for a 500x increase in computing time) provides only a modest additional increase in accuracy, which confirms that a single pre-phased configuration provides nearly as much accuracy as much more compute intensive methods for capturing haplotype uncertainty. These results suggest that pre-phasing is a good general strategy for genome-wide imputation, while slower but more accurate approaches may be useful for follow-up analyses near putative disease loci.
