A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
Only duos that were part of an informative pedigree were used. Top: The mean number of recombinations per meiosis (for all informative duos from all cohorts) found for each chromosome against the expected number (from the 2002 deCODE map) for paternal meioses (left) and maternal meioses (right). Merlin's values are substantially inflated whilst SHAPEIT2's are more consistent with the well known deCODE map genetic lengths. Bottom: Q-Q plots for the observed against expected number of recombinations estimated by each method for paternal meioses (left) and maternal meioses (right). For the expected distribution of recombination rates, a Poisson distribution using the genetic lengths from the 2002 deCODE Map was used (with rate parameter 42.81 and 25.9 for maternal and paternal recombinations respectively). SHAPEIT2's rates are less inflated than those of the Merlin.