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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.


Population genetics


  • Operation: Phasing; Imputation
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 5.1
  • Maturity: Mature
  • Credit: Wellcome Trust, University of Auckland Research Committee, National Institutes of Health (NIH), National Human Genome Research Institute of the National Institutes of Health
  • Contact: Brian Browning browning _at_
  • Collection: -


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.
PMID: 17924348
PMCID: PMC2265661

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.
PMID: 19200528
PMCID: PMC2668004

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.
PMID: 30100085
PMCID: PMC6128308

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