The generation of IBD matrices with microsatellite markers has been addressed through a number of different techniques. We are using multipoint IBD (mIDB) as our standard because of the low information provided by a single SNP. Although a new version of GENEHUNTER [7] has recently been released to deal with SNP markers, the large size of some of these pedigrees required extensive trimming because the basic algorithm still computes all possible inheritance vectors. We therefore decided to use the LOKI software to generate IBD matrices.
