====== eagle ======
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. 

===== Information =====

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

===== Usage =====

See which versions are available:
<code>$ module avail eagle</code>

Load one version into your environment and run it:
<code>$ module load eagle/2.4.1
$ eagle</code>

===== Installation ======
Notes from the sysadmin during installation.

<code>$ 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</code>