haplotypes that are similar to those in a study population but do not carry a variant allele that segregates in that population, and (iii) misleading results from reference haplotypes that carry recurrent mutations. We discuss these issues in File S5; we conclude that they will seldom hurt the imputation of low-frequency alleles from HapMap 3 or 1000 Genomes haplotypes, but that reference panel composition may need to be reevaluated when imputing rare alleles (MAF < 0.5%) or using other reference datasets.
