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How to do GWAS in the cloud using Amazon Web Services

Genome-wide association studies (GWAS) offer a way to rapidly scan entire genomes and find genetic variation associated with a particular disease condition.

Our aim is to teach researchers how to perform genome wide association analysis using Amazon Web Services (AWS). This tutorial will enable researchers with minimal bioinformatics background to set up and access an AWS instance, move data in and out of the AWS instance, run some basic summary statistics and perform a simple association analysis starting with variant calling files (.vcf). We will also produce Manhattan plots to visualize variants associated with traits.

For this tutorial, we will not work with human data. We will use coat color in dogs as the trait of interest (instead of disease), and test the association of a genome-wide set of single nucleotide polymorphisms (SNPs) with two coat color variants: yellow and dark. To extrapolate this tutorial to human disease data, you might consider yellow coat color phenotype as the "case" (or disease) and dark coat color as the "control" (or normal) condition.

This tutorial is based on the ANGUS 2017 GWAS tutorial

Table of contents

Est. Time Lesson Name Description
10 mins What is GWAS? Background
20 mins Set up an AWS instance How to set up an amazon web services instance
40 mins Download and move data to AWS Download dog coat color data and use terminal to access data on remote computer
10 mins Install PLINK Install the software PLINK
10 mins Install VCFtools Install the software vcftools
10 mins Install R and RStudio Install the software R and RStudio
10 mins Analyze Generate summary statistics and association analysis
20 mins Manhattan Plots Make some plots to visualize data
10 mins Terminate AWS Instance Shut down the cloud computer

Learning Objectives

  • learn to set up and access Amazon Web Services
  • learn to move data in and out of the AWS instance
  • learn to install and run all software necessary for GWAS analysis
  • learn to produce Manhattan plots
  • Background: Some expertise in biology and fundamental genetics.
  • Technology: Basic shell scripting knowledge and access to MacOS. Users must be comfortable with finding and opening a terminal window, navigating to specific directories and running pre-scripted commands in the terminal.
  • Financial: First time AWS users require a valid credit card to set up an AWS account.
  • Time: AWS account setup needs approval by AWS, and approval times can range from minutes to days.

Last update: October 10, 2020