State space decomposition. A pedigree for a small set of half-sibs, including parents and one set of grandparents known. In Merlin (left) , all meioses, i.e. all allele transmission, are covered by the state representation in a single stochastic process. In our model (right), on the other hand, the pedigree is decomposed into a series of focus pedigrees, with one individual and its immediate ancestors k generations back. Here, k=1. Some individuals in this pedigree then appear in up to 6 unique focus pedigrees. Parameter values representing phase and unknown genotypes are shared among all focus pedigrees. Thus, global information on allele transmission is inserted into the individual focus pedigrees, while avoiding the exponential explosion in the size of the state space resulting from explicitly keeping track of all meioses at once, as is done in e.g. Merlin.
Nettelblad BMC Genetics 2012 13:85 doi:10.1186/1471-2156-13-85