A coalescence-guided hierarchical Bayesian method for haplotype interface

A novel haplotype-inference method based on a coalescence-guided hierarchical Bayes model is reported, where a hierarchical structure is imposed on the prior haplotype frequency distributions to capture the similarities among modern-day haplotypes attributable to their common ancestry. Coalescence-based simulation and empirically generated data sets are used to demonstrate the merits of the new method in comparison with HAPLOTYPER and PHASE, with or without the presence of recombination hotspots and missing genotypes.