Why are haplotype frequencies from PBAT different than those from Haploview and Phase2?
PBAT computes haplotype frequencies differently than Haploview and Phase2. Based on the observed offspring haplotypes, a possible set of parental haplotypes are constructed. Only those parental haplotypes that are consistent with the offspring haplotypes are retained. For example, if the offspring haplotypes are unphased, only parental haplotypes that produce unphased offspring haplotypes are retained. Once the *consistent* parental haplotypes are imputed, the probability of transmission is computed for each possible parental haplotype configuration (which assumes Mendelian transmission). For unphased haplotypes in offspring, the haplotype frequencies are based on family information as well, so the frequencies can be different across programs. Haploview and Phase use population-based methods (as does HelixTree using the Haplotype Frequency Estimation Viewer) to obtain haplotype frequencies. That is, for subjects who are unphased, a distribution of possible haplotypes is imputed, and ea
