Welcome to the SNP Genome-Wide Association Tutorial!¶
Updated: February 24th, 2017
Version: 8.7.0 or higher
The following tutorial is designed to systematically introduce you to a number of techniques for genome-wide association studies. It is not meant to replicate all the workflows you might use in a complete analysis, but instead touch on a sampling of the more typical scenarios you may come across in your own studies.
The genotype data included is a portion of a public GWAS dataset from the Gene Expression Omnibus database, as well as 270 HapMap samples. There is a population spreadsheet that identifies the HapMap subpopulation and the study data. Both studies were run on the Affymetrix 500K genotyping array. All phenotype data is simulated.
To follow along you will need to download and unzip the following file:
We hope you enjoy the experience and look forward to your feedback.
All open windows (except the Project Navigator) can be closed after each section’s completion.
- 1. Sample QA - I: Basics
- 2. Sample QA - II: Cryptic Relatedness
- 3. Sample QA - III: Population Stratification
- 4. SNP Quality Assurance
- 5. Genotype Association Analysis