The Eagle software estimates haplotype phase 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 and a rapid search algorithm that explores only the most relevant paths through the HMM. Compared to the Eagle1 algorithm, Eagle2 has similar speed but much greater accuracy at sample sizes <50,000; as such, we have made the Eagle2 algorithm the default option. (The Eagle1 algorithm can be accessed via the –v1 flag.) Eagle v2.3+ supports phasing sequence data with or without a reference and also supports phasing chrX.

• Version: 2.4.1
• Added: June, 2022
• Link: https://alkesgroup.broadinstitute.org/Eagle/

See which versions are available:

$ module avail eagle

Load one version into your environment and run it:

$ module load eagle/2.4.1
$ eagle

Notes from the sysadmin during installation.

$ cd /tmp
$ wget https://storage.googleapis.com/broad-alkesgroup-public/Eagle/downloads/Eagle_v2.4.1.tar.gz
$ tar xf Eagle_v2.4.1.tar.gz
$ sudo mkdir -p /export/apps/eagle
$ sudo cp -r Eagle_v2.4.1 /export/apps/eagle/2.4.1