Chunk #32 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Detecting recombination events
calculation. A recombination event is inferred whenfor some threshold . In the analysis in this paper we have used . To calculate these probabilities we tried using SHAPEIT2's most likely (pedigree corrected) haplotypes, or sampling haplotypes from SHAPEIT2's diploid graph (again correcting for pedigree structure) and repeatedly calculating recombination probabilities and averaging the resulting maps. We find that both these methods produce similar results (data not shown) and we only report results from the sampling based approach.
