Fig. 4

Statistical methods for crossover detection using a hidden Markov model. a The true haplotypes of the markers (h1, h2) are unknown, and the transitions between haplotype states are modeled by a hidden Markov model. The genotypes are observed from data and are controlled via an emission model b. Integrating information from the observed data, the transition model, and emission model, the most likely true haplotype sequence is inferred. b Example of a missing markers in Gamete 2 and Gamete 4. In Gamete 4 missing data for marker m4 creates ambiguity in crossover identification. Statistical inference methods can be used to probabilistically assign crossovers to the subinterval where information is missing