We merged the pedigree founders with individuals who were not in any explicit pedigree for each cohort, that is, all non-founders from pedigrees were excluded. This gave us a sample of (nominally) unrelated individuals that we phased using each of the methods. We applied SLRP (version 09f0f52), SHAPEIT2 (r613), Beagle (version 3.3.2) and HAPI-UR (version 1.01) to these founder data sets. We then calculated the switch error (SE) [34] of the haplotype estimates for the pedigree founders, treating the Merlin haplotypes as the truth. This evaluation pipeline is visualised in Figure S4.
