BEAR Applications

EIGENSOFT 7.2.1-foss-2019a

There is a newer version of EIGENSOFT

The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (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.

Accessing EIGENSOFT 7.2.1-foss-2019a

To load the module for EIGENSOFT 7.2.1-foss-2019a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load EIGENSOFT/7.2.1-foss-2019a

BEAR Apps Version

2019a

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

• BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
• BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

More Information

For more information visit the EIGENSOFT website.

Dependencies

This version of EIGENSOFT has a direct dependency on: foss/2019a GSL/2.5-GCC-8.2.0-2.31.1 Perl/5.28.1-GCCcore-8.2.0

Other Versions

These versions of EIGENSOFT are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 11th February 2020