Germline

GERMLINE is an algorithm for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing.

GERMLINE uses a novel hashing & extension algorithm which allows for segment identification in haplotype data in time proportional to the number of
individuals. Presently, GERMLINE can execute on phased or un-phased data; though we have found performance much improved with phasing while phasing &
running GERMLINE is still significantly faster than comparable IBD algorithms. Utilities for easily phasing data for GERMLINE are available below. GERMLINE can identify shared segments of any specified length, as well as allow for any number of mismatching markers.

The program has been developed in Itsik Pe'er's Lab of Computational Genetics at Columbia
University. It is built in C++ and tested in the Red Hat Linux environment; the source is distributed here in a tar.gz package under the GPL license.
If you use GERMLINE in a published analysis, please cite Gusev
A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I (2008) Whole population, genomewide mapping of hidden relatedness.
Genome Research.