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The American Journal of Human Genetics

Segments of identity by descent (IBD) are used in many genetic analyses. We present a method for detecting identical-by-descent haplotype segments in phased genotype data. Our method, called hap-IBD, combines a compressed representation of haplotype data, the positional Burrows-Wheeler transform, and multi-threaded execution to produce very fast analysis times. An attractive feature of hap-IBD is its simplicity: the input parameters clearly and precisely define the IBD segments that are reported, so that program correctness can be confirmed by users.

A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data