7.1 Introduction to ibddrop

ibddrop estimates probabilities of gene identity by descent, ibd, (such as kinship, inbreeding, or multi-gene identities) by Monte Carlo in the absence of data. Given the pedigree and a genetic map, ibddrop simulates meioses indicators and scores them to estimate the ibd probabilities among a set of gametes.

The simplest example of estimation of ibd probabilities among a set of gametes is the computation of an individual's inbreeding coefficient. In this example, the set of gametes in question are the maternal and paternal gametes that make up the individual. A set of two gametes can be either ibd or not-ibd. To keep track of ibd status among the gametes, we can label the paternal allele `1'. If the two alleles are ibd, the maternal allele would also be labeled `1', and the resulting ibd pattern would be `1 1'. If the two alleles are not ibd, the maternal allele would be labeled `2' and the resulting pattern would be `1 2'. The individual's inbreeding coefficient is the probability that the two alleles follow the `1 1' pattern.

If there are three gametes in the set, there are five potential ibd patterns: `1 1 1' (all three gametes are ibd), `1 1 2' (the first two are ibd and the third is not), `1 2 1' (the first and third are ibd) , `1 2 2' (the last two are ibd), and `1 2 3' (none are ibd). ibddrop can estimate probabilities of ibd patterns among up to 10 gametes in a set. ibddrop outputs a probability for each ibd pattern at each marker.

Gene identity can be scored either for each locus separately, in which patterns of identity among up to ten haplotypes can be scored, or it can be scored jointly over a moving window of several loci. If the moving window option is selected, genedrop calculates the probability that the specified pair of gametes are ibd at all loci in the window. As a result, it is then possible to determine the probability that all or some of the gametes are ibd for a particular haplotype.