We utilised male chromosome X haplotypes as the basis for these simulated datasets. Since males only have one copy of chromosome X, phase is unambiguously known. As in previous phasing studies [2], [43], [44], two male X chromosomes were combined to create a pseudo autosomal diploid founder individual where the true underlying haplotypes are known. We then randomly mate these new diploid individuals to produce offspring with recombined haplotypes. Crossover events were simulated as a Poisson process on the genetic lengths from the HapMap Chromosome X genetic map for females and the same map scaled by 0.605 for males (difference in rates estimated from 2002 deCODE Map).
