Outside Variants Repository

In this repository is the code for the analysis pipeline accompanying the paper: Cell type specificity of intralocus interactions reveals oligodendrocyte intrinsic mechanisms for multiple sclerosis (Corradin et al, 2019)

The main component is a script to predict loci that significantly alters genetic risk when acting in conjunction with the putative GWAS loci for a trait.

In order to download the scripts, you should clone this repository via the commands

git clone https://github.com/corradin-lab/outside-variants.git
cd outside-variants

In order to install the Python dependencies, you will need the Anaconda Python distribution and package manager. After installing Anaconda, run the following commands to create an environment with dependencies:

conda env create —file environment.yml
source activate OVP_env

Once the above has completed, you can run:

python_scripts/OVP_script.py -h

to print a list of all command-line options. If these commands fail with an error, then something as gone wrong during the installation process.

To do a walk-through tutorial on how to use the scripts and the format of inputs/outputs, click here

To learn about the theoretical framework of our approach, click here.