Installation Instructions

Installation Instructions

Requirements

GNetLMM requires Python 2.7 with scipy, h5py, numpy, pylab and LIMIX.

GNetLMM can use Plink 1.9 to calculate the genetic relatedness matrix from bed genotype files. If Plink 1.9 is not found, a python implementation is used. We strongly recommend using Plink 1.9 for large genotype files.

Installation

The repository can be cloned using git

git clone https://github.com/PMBio/GNetLMM.git

GNetLMM can be run from the command line using the scripts in GNetLMM/bin as standalone software as shown in the tutorial.

Operating system

GNetLMM has been tested on Mac OS X and Linux. If you have any trouble installing it, please contact us.

How to use GNetLMM

Please find instructions and examples in the tutorial.