To illustrate how important GLPhase was to genotype calling and phasing on such a large sample size, we carried out a comparison to Beagle 3.1, Beagle 4.1 and the original SNPTools method. We ran all four methods on five randomly selected 1024 site chunks from chromosome 20 on the cluster using increasing sample sizes and measured run time. Supplementary Figure 6 shows that GLPhase is approximately 100 times faster than the next quickest method at the full HRC sample size.
