A Hands-on Introduction to GWAS

Pieter Clauw
, June 2022

[email protected]


Presentation slides

A hands-on introduction to GWAS

How to run this activity

The activity on sweep detection will be run through Jupyter Notebooks. So, just as in the introductory tutorial on Python and Jupyter Notebooks by Hannes Svardal, you will first need to start a Jupyter Notebook on your AWS instance and connect to it.

Connect to the instance using SSH. Use “wpsg” as the username and the usual password. You can do that either through Guacamole in your web browser:

Or you can use SSH from your terminal:

Once connected through SSH:

  • Navigate into the tutorial directory: cd ~/workshop_materials/a10_gwas
  • Start a screen session by typing: screen
  • Confirm with the “Return” key
  • Start the conda virtual environment: conda activate limix
  • Start the notebook server: jupyter notebook --no-browser --port=8889
  • The command blocks the terminal. That is normal. Keep it running. You can get back to a functional terminal by typing “Ctrl + a, d” (first “Ctrl + a”, then “d”)
  • In your local browser, navigate to the web address: http://ec2-XXX-XXX-XXX-XXX.compute-1.amazonaws.com:8889 (replace XXX with your Amazon instance IP address
  • Then you should see see the contents of the folder in which your instance is running.

 

Instructions for Independent Work

Please follow the instructions in this pdf .