The first advantage of this approach is that the relatedness between the extended set of genotyped samples leads to a very accurate phased scaffold. For the analysis in the paper this set included 392 mother-father-child trios, 30 parent-child duos and 905 nominally unrelated samples. The phasing of trios and duos is expected to be highly accurate due to the Mendelian constraints on the underlying haplotypes. The phasing of the unrelated samples will benefit from being phased together with these trios and duos. The second advantage is that the phasing of the GL data onto the scaffold is carried out in chunks. Since the variants in each region are phased ‘onto’ the scaffold no further work is needed to combine the regions together. As such, the method is highly parallelizable. This approach generalizes our MVNcall [9], approach which is designed to phase one variant site at a time onto a haplotype scaffold, and improves upon it’s accuracy, by phasing multiple sites jointly onto the scaffold and using a more sophisticated underlying model.
