This is an introduction to imputation and imputation-based association studies using IMPUTE2. Prerequisites that are assumed are some familiarity with the unix shell.
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
- Max Winston
- Ittai Eres
- John Novembre
- Arjun Biddanda