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An algorithm for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. GERMLINE 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.

Software type:
Command line interface
Restrictions to use:
Operating system:
Computer skills:
GERMLINE version 1.5.1
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  • (Gusev et al., 2009) Whole population, genome-wide mapping of hidden relatedness. Genome research.
    PMID: 18971310

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