We initialise some of the genotypes by using the genotype posteriors P (Gl|H, R) provided by the Beagle phasing model. Our approach relies on fixing the genotypes with high posterior probabilities and then use our model to call all the remaining genotypes (Supplementary Fig. 3b). Fixing highly confident genotypes is beneficial as it implies additional constraints on the space of possible haplotypes. In practice, segments then tend to contain more sites than in the default model: 32 sites on average per segment when applied to 1000GP instead of only 3 sites if no genotypes are fixed.
