Welcome to the LD and Haplotype Analysis Tutorial!¶
Updated: November 4th, 2011
Level: Intermediate
Modules: HelixTree
Contents: Jump to Table of Contents
This tutorial leads you through various LD and haplotype analyses in SVS 7. For demonstration purposes, a simulated dataset is used consisting of actual Affymetrix 500K genotypes from the four HapMap populations (Phase II) and a fake case/control status.
By completing this tutorial you will learn how to:
- Generate and compare multiple LD plots
- Automatically and manually define haplotype blocks
- Produce haplotype frequency tables
- Compare single marker and haplotype association results
Caution
This tutorial does not cover quality assurance and therefore no quality assurance steps have been performed on the data. As it may be appropriate to filter markers out of Hardy-Weinberg Equilibrium or with low call rates and minor allele frequencies, it is recommended that you perform such measures with your own data prior to performing LD and haplotype analysis.
Requirements
To follow along you will need to download and unzip the following file, which includes several datasets:
Download
We hope you enjoy the experience and look forward to your feedback.
Table of Contents:
