EIGENSOFT

Software name: 
EIGENSOFT
Policy 

EIGENSOFT is freely available to all users of HPC2N.

General 

The EIGENSOFT package combines functionality from the population genetics methods described by Patterson et al. 2006 and the EIGENSTRAT stratification correction method described by Price et al. 2006.

Description 

The EIGENSOFT package combines functionality from the population genetics methods described by Patterson et al. 2006 and the EIGENSTRAT stratification correction method described by Price et al. 2006. The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

New features of EIGENSOFT 6.x include fastmode option which implements a very fast pca approximation (Galinsky et al. 2016a, Galinsky et al. 2016b) and support for multi-threading. EIGENSOFT 6.1.4 includes bug fixes for pcaselection and a better out of memory diagnostic message.

Availability 

On HPC2N we have EIGENSOFT available as a module on Abisko.

Usage at HPC2N 

To use the EIGENSOFT module, first add it to your environment. Use:

module spider eigensoft

to see how to load the module and the needed prerequisites.

Example, loading EIGENSOFT version 6.1.4

ml icc/2017.1.132-GCC-6.3.0-2.27 
ml impi/2017.1.132
ml EIGENSOFT/6.1.4

You can read more about loading modules on our Accessing software with Lmod page and our Using modules (Lmod) page.

Additional info 

More information about EIGENSOFT can be found on their homepage.

Updated: 2017-11-22, 19:57