Fast-LMM

Overview

Fast-LMM [Factored Spectrally Transformed Linear Mixed Models] from Microsoft Research, is a Python module for performing both single-SNP and SNP-set genome-wide association studies (GWAS) on extremely large data sets.

Version 0.2.31 is installed on the CSF.

Restrictions on use

This software is open source (via the Apache License 2.0) so all CSF users may access it.

Set up procedure

To access the software you must first load the modulefile:

module load apps/gcc/python-packages/anaconda-2.5.0/fastlmm/0.2.31

Note: this will automatically load anaconda python 2.5.0 (which provided Python 2.7) for you.

Running the application

Please do not run Fast-LMM on the login node. Jobs should be submitted to the compute nodes via batch.

Batch job submission

After loading the moduelfile above, please write a job submission script and use qsub to submit it to the system. For example:

#!/bin/bash
#$ -cwd
#$ -V
python myscript.py

Further info

• Fast-LMM website