Figure 1. Schematic of the methods underlying rhapsodi (R haploid sperm/oocyte data imputation).

Low coverage data from individual gametes (A) is clustered to phase the diploid donor haplotypes (B). A Hidden Markov Model, with tunable rates of genotyping error and meiotic crossover, is applied to trace the most likely path along the phased haplotypes for each gamete (C) thereby imputing the missing gamete genotypes (D) which can be used to discover meiotic recombination events as transitions from one donor haplotype to the other (e.g., purple [H2] to teal [H1] in gamete G4 between SNPs 7 and 8).