As part of a new hire workshop series at the Analytic and Translational Genetics Unit (ATGU), Massachusetts General Hospital, we decided to introduce Hail as a genomics analysis tool. This git repo contains the workshop materials for analysing common (GWAS) using Hail.
Lead: Edmund Higham
TA: Patrick Schultz, PhD
Before we begin, Hail depends on Java 8 or 11. Please ensure you have either installed. You can download a JDK for your platform here.
In the following steps, we assume you're using MacOS and ZSH.
We'll start by cloning this repository and then setting up a python 3.9 virtual environment.
$ git clone [email protected]:hail-is/ATGU-Hail_Workshop2023.git
$ cd ATGU-Hail_Workshop2023
We'll then set up a python virtual 3.9 environment and install hail. We'll use pyenv select the python version
$ brew install pyenv
$ eval "$(pyenv init -)"
$ pyenv install 3.9
$ pyenv local 3.9
(Optional) Set up a virtual environment for this repository only:
$ python -m venv .venv
$ source ./.venv/bin/activate
Then install hail and jupyter
$ pip install hail jupyter
You can use vscode with the python extension or explore the tutorial notebook in your browser:
$ jupyter notebook
Date: September 12th, 2023
Slide deck: CommonVariantAnalysisHail.pdf
Jupyter notebook: ATGUworkshop_CVanalysis.ipynb
The resources folder contains the files needed to run the Jupyter notebooks.