Computing conditional recombination probabilities given marker information.

When a parent is homozygous, it is not possible to determine directly whether offspring share an allele identical by descent (IBD) from that parent. However, an IBD probability can be computed using information from linked loci where the parent is heterozygous. To solve this problem for the phase-known case, probability equations and a computer program were developed for efficient computation of conditional probabilities under a Sturt model of chiasma interference. Data are analyzed and contrasted with and without taking interference into account. The effect of failing to account for interference is very small, but the computational cost is also small.