brimittleman/imputation_exercise

Introductory Workshop for Imputation and GWAS

imputation_exercise

Introduction

This is an introduction to imputation and imputation-based association studies using IMPUTE2. Prerequisites that are assumed are some familiarity with the unix shell.

Setup

In order to setup the working environment for this workshop, we will be using git and anaconda in order to setup our environment.

To get started, run:

git clone https://github.com/NovembreLab/imputation_exercise
cd imputation_exercise

Then we install miniconda, which will allow us to maintain all of the dependencies in our working environment.

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
chmod 755 Miniconda2-latest-Linux-x86_64.sh
./Miniconda2-latest-Linux-x86_64.sh

Afrer agreeing to everything that the installation of conda asks you to do, run:

source ~/.bashrc
conda env create -f imputation_exercise_environment.yml

And finally:

source activate imputex

To get out of the setup environment, type:

source deactivate

Acknowledgements

• Max Winston
• Ittai Eres
• John Novembre
• Arjun Biddanda