Welcome to the LD and Haplotype Analysis Tutorial!

_images/association-ld-chr22.png

Updated: March 8, 2014

Level: Intermediate

Packages: SNP Analysis, Power Seat

This tutorial leads you through various LD and haplotype analyses in SVS 8. For demonstration purposes, a simulated dataset is used consisting of actual Affymetrix 500K genotypes from the four HapMap populations (Phase II) mapped to the hg19 Human reference build GRCh_37, simulated case/control status and simulated quantitative phenotype.

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 based on Hardy-Weinberg Equilibrium or those 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:

We hope you enjoy the experience and look forward to your feedback.