Figure 2

Illustration of model. Panels, from top to bottom: 1) In a focus pedigree, the skewness parameters γ _mi per marker per individual determine chromatid assignment of the recorded alleles. A state bit s _i per individual in the pedigree (except for the focus individual) determines which chromatid was transmitted to the offspring. Here, we see a recombination after the fourth marker in an imagined state sequence. The alleles listed in the figure should be interpreted as the actual emitted symbols. 2) In every non-founder in the focus pedigree, the shuffling flag σ _i maps the two chromatids to parental origin. Here, chromatid 1 is defined as originating from the parent shown in the panel above. 3) By introducing sureness values $â$, any recorded allele value can be treated as not fully definite. In an iterative refinement, the genotypes can be inferred, going from low information to an almost definite assignment. This is useful both for handling genotyping errors and for inferring missing genotypes.