A general hidden Markov model for multi-parent populations

A common step in the analysis of multi-parent populations is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a model for the exchange process along chromosomes, including the relative frequency of founder alleles and of the probability of exchanges among them. While the precise experimental design used to generate the population may be used to derive a precise characterization of the exchange process, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of multi-parent populations. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly available data on Diversity Outbred and Collaborative Cross mice.