Tag Archives: haplotypes

Tip of the Week: HapMap data in Haploview

HapMap has had a few minor updates to their browser, and importantly, new phase 3 data was released early last year (drafts of that data were released in 2008). Haploview, the downloaded software that allows the user to perform in depth LD and haplotype analysis, has been recently updated from version 4.1 to version 4.2. Haploview can be used with user data or data downloaded from the HapMap project. Though, version 4.1 did not work for phase III HapMap project data, so the user had to use phase I and II data if they wanted to use version 4.1. Haploview has now been updated to version 4.2, allowing the user to use HapMap phase III data.

That’s a lot of versions and phases :). The short of it is, if you use Haploview 4.2, you can view and analyze data from any phase of the HapMap project.

Today’s tip briefly shows you how to download data from the HapMap project and view it in Haploview.

Pedigree drawing software

A question across the MGI mailing list this weekend was: “Is there a good, easy to use template/program for drawing pedigrees that someone could recommend?”

So far the suggestions include:
Pedigree Draw: http://www.pedigree-draw.com/ A mac-only tool available for purchase.

Pedigree Viewer: http://www-personal.une.edu.au/~bkinghor/pedigree.htm is a free tool, for Windows.

Another suggestion came for HaploPainter: http://haplopainter.sourceforge.net/html/index.html this for installation on Windows/linux, but also can be installed on Macs with a bit of awareness about the installation process. The diagram with the HaploPainter page looked really nice, so I went to check out the paper. Thiele and Nürnberg were challenged by some genome-wide scans with over 10,000 SNPs that they wanted to display. They created this software to solve their problem, and released it for others use as well. Looks like it could be really useful–we will have to test it out.

If anyone has other suggestions, add them here and I can send them back to the mailing list–or, of course, you can sign up yourself!

EDIT: here’s another nice looking program submitted to the MGI mailing list: http://eyegene.ophthy.med.umich.edu/madeline/index.php Madeline 2.0

Progeny: this company has software that people have told us they like. I just realized they had a free pedigree tool that you can check out: http://www.progenygenetics.com/students/

I just remembered another project that I had heard about–the Surgeon General’s Family Health project has a tool for family medical history pedigrees: https://familyhistory.hhs.gov/ My Family Health Portrait.

PediDraw–found another one, and I’ll keep adding them as I find them.  This is a web-based tool.  The paper accompanying this one is available in PubMedCentral.

Thiele, H. and Nürnberg, P. (2004). HaploPainter: a tool for drawing pedigrees with complex haplotypes. Bioinformatics, 21(8), 1730-1732. DOI: 10.1093/bioinformatics/bth488