EIGENSOFT is freely available to all users of HPC2N.
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.
On HPC2N we have EIGENSOFT available as a module on Abisko.
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
More information about EIGENSOFT can be found on their homepage.