Eagle v2.3.2

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, the Eagle2 algorithm is now 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.

Accessing the software

To load the module:

$ module load apps/eagle/v2.3.2

Run the following command to view command line options for Eagle:

$ eagle --help

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the website for more information regarding this application.


Last modified: 02 August 2017