We have found that the resulting haplotypes from our method are so accurate that we can infer recombination events in parent-child duos. We use the output of our duoHMM to estimate the probability that a recombination event occurs between each pair of heterozygous markers. When applied to all eight cohorts across whole chromosomes we find that the number of recombination events inferred by our method shows close agreement with the genetic length of each chromosome. We also find that the observed number of recombination events per individual closely matches what we expect to observe based on genetic map estimates. These results are also much better than those produced from Merlin, which shows elevated rates of recombination events across all chromosomes. On realistic simulated data our method (TPR = 92.4%, FDR = 3.78%) substantially outperforms Merlin (TPR = 90.57%, FDR = 62.48%).
