GERMLINE is a program 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. GERMLINE can identify shared segments of any specified length, as well as allow for any number of mismatching markers.

GERMLINE was developed in Itsik Pe'er's lab at Columbia University. GERMLINE website.

For large numbers of Germline jobs, use Germline on Biowulf.

Sample session

[user@helix myproject]$ germline
Please indicate which file format you'll be using for individuals
     Enter 1 for PED / Plink
     Enter 2 for PHASE / HapMap
1
Please enter the MAP file name
CEU.22.map
Please enter the PED file name
CEU.22.ped
Please indicate output file location: 
newtest
0 SNPs have genetic distance
Read Markers
100%
Match Markers
100%

[user@helix myproject]

Documentation

Germline website and documentation.