We use the realistic dataset to compare three different versions of our method for phasing extended pedigrees. First we applied SHAPEIT2 ignoring all pedigree information. Secondly, we applied our duoHMM method to this set of haplotypes to correct SEs. We also used the duoHMM output to identify positions where there was strong evidence of genotyping error, and we investigate the effect of excluding these sites for accuracy comparisons. Finally, we applied our method of partitioning the extended pedigrees into trios and duos and then ran Beagle using this level of family information. We also evaluate Merlin's haplotype accuracy on this simulated data.
