Figure 1.

Diagram of process for imputing missing genotypes. We first construct a hidden Markov model (HMM) based on the progeny genotypes to estimate founder haplotype probabilities across the genome. Then at each position, for each missing founder, we audit genotypes among progeny inheriting that founder haplotype. The most common genotype inherited in those progeny is imputed in the founders. The imputed founders are then used as a reference panel to impute missing progeny data by summing HMM probabilities for possible alleles.