Hapmap--percent common variation explained

Question

[kbountre]

Hi--

I'm new to hapmap and wondered how to figure out what % of the common variation in a gene I'm able to explain using the SNPs that I have genotyped. Does anyone know if this is possible in hapmap, and if it is, how to do this?

Thank you!!

Katie

Answer 1

[christopher medway]

You can use Haploview. If you take a look at the 'tagger' function, it allows you to select a panel of 'tagging SNPs' (i.e the ones you have genotyped) and 'captured SNPs' (i.e all the variation within the gene). You give it an r2 threshold, and it will use HapMap data (or any other data you upload) to calculate how much of the variability you have captured with your set.

[kbountre]

Thank you so much! Very helpful!

[bountres]

I have just a couple follow up questions:

--I'm having trouble figuring out what information goes where on the Tagger website [https://www.broadinstitute.org/mpg/tagger/server.html]. Do the coordinates for the SNPs I have genotyped go in "chromosomal landmarks"? Or do they go in "include tag SNPs"? When I put their coordinates or the SNP rs #s in either of those spaces (respectively), I get this error message: Linux env: /broad/lsf/7.0/linux2.6-glibc2.3-x86/bin/bsub: No such file or directory.

--If that isn't the place to put the SNPs I have genotyped, where should that go?

--Aside from the information you would enter as part of my first question, what other information needs to be added?

Sorry, and thank you for your help!