Beagle is a tool for genotype calling, phasing, identity-by-descent segment detection, and genotype imputation. The Beagle algorithm uses a modified version of the Li and Stephens haplotype frequency model that reduces the space requirements and a pre-processing step that re-computes an original reference panel into a composite reference haplotypes. These steps reduce both space and computing time.
Browning SR, Browning BL "Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering." Am J Hum Genet. 2007 Nov;81(5):1084-97. Epub 2007 Sep 21. https://doi.org/10.1086/521987
Browning BL, Browning SR "A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals." Am J Hum Genet. 2009 Feb;84(2):210-23. https://doi.org/10.1016/j.ajhg.2009.01.005
Browning BL, Zhou Y, Browning SR "A One-Penny Imputed Genome from Next-Generation Reference Panels." Am J Hum Genet. 2018 Sep 6;103(3):338-348. 2018 Aug 9. https://doi.org/10.1016/j.ajhg.2018.07.015
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