Supported Applications


  • Description

    The Eagle software estimates haplotype phase [1] either within a genotyped cohort or using a phased reference panel. Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new, very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas: a new data structure based on the positional Burrows-Wheeler transform [2] and a rapid search algorithm that explores only the most relevant paths through the HMM.

  • Primary Citation*

    P. R. Loh, P. Danecek, P. F. Palamara, C. Fuchsberger, Y. A. Reshef, H. K. Finucane, S. Schoenherr, L. Forer, S. McCarthy, G. R. Abecasis, R. Durbin, and L. P. A.. 2016. Reference-based phasing using the Haplotype Reference Consortium panel. Nat Genet. 48(11): 1443-1448.

    • *Full citation information available through

  • Keywords


  • Default Versions

    Linux 64:  2.4.1