Julia Krushkal

Computer Assignment for Module 3 - HapMap Project Module, MSCI815

April 17, 2008


1. We will us examine the data viewing and analysis with Haploview.

We will use the Haploview tutorial, available from Broad Institute at http://www.broad.mit.edu/mpg/haploview/tutorial.php. This program was developed by Barrett, Julian Maller and David Bender in Mark Daly’s group.


Log into your computer

Open Start

Follow these links to the following folders

My Documents ->Haploview ->Haploview


Click on Haploview (the program)


We will use the following example files:


a Linkage format file containing genotype information for 20 markers across 40 trios (120 total individuals) as well as some relevant family information


an info file containing the names of the markers and their positions

Both of these files are excerpted from the IBD 5q31 region described by Rioux et al. (A Crohn’s disease susceptibility locus, additional information about it is available from http://www.broad.mit.edu/humgen/IBD5/ )

You may also review other available file formats (e.g., PLINK, PHASE, etc. ) by following this link:


With the Haploview program runnig, click on File -> Open new data ->select Browse ->click on sample.ped  

Make sure that sample.info is selected as the Locus information file.

Click “O’K”

This will open your example data set in default linkage format.

We will now follow the steps from the attached HapMap tutorial (http://www.broad.mit.edu/mpg/haploview/tutorial.php.)


You may view the relative location of SNPs, haploblocks, and genes in this region on 5q31 of suggested susceptibility to Crohn’s disease from http://www.broad.mit.edu/humgen/IBD5/haplodata.html

These data are from Rioux et al. (Nature Genetics 29, 223-228, Oct 2001)


2. Now view the HapMap genome browser at http://www.hapmap.org/

Select “5q31” under “Landmark or Region” and click on “Search

Under “Scroll/Zoom”, choose “200 kbp

Under “Reports and Analysis” select “Highlight SNP properties

Click “Go”, then “Configure”. This will demonstrate relative location of SNPs in this region and their properties

Now select “Annotate LD plot”, and click on “Go” and “Configure”

Now select “Download phased haplotype date” and click on “Go”

You will be able to view phased haplotypes.

You can also experiment with downloading genotype data and LD values