Rare SNPs are of particular interest because of an increasing awareness that such SNPs may underlie common, complex diseases, and because imputation methods gain the most power over tagging approaches at such SNPs [6],[11]. Expanded reference panels ought to allow rare SNPs to be imputed much more accurately than they can be with the HapMap panel, and our method is able to exploit this information more effectively than competing methods. Relative to IMPUTE v1 (which had access to only the HapMap reference panel) and BEAGLE, the main improvement of IMPUTE v2 is to increase specificity by cutting down on false positive heterozygous calls; relative to fastPHASE and PLINK, the main improvement is to increase sensitivity by cutting down on false negative heterozygous calls.
