File Containing LD-Pruned SNPs with MAF in CEU and YRI populations?

Question

[vlaufer]

Hello,

Calculation of Local Ancestry normally requires information about the Ancestral Populations, information about the LD structure, or both.

However, since a large number of people have all worked on this exact problem, I think it is probably likely that there is a pre-pruned, pre-compiled list of AIMs available somewhere on the interwebs. Does anyone know where to find such? I am working with sequencing data of persons with African-American Ancestry.

Answer 1

[Katie D'Aco]

There are a few papers that have published lists of AIMs, but as far as I know there is no standard set. The list of AIMs depends on which populations you are looking to distinguish. I've had luck searching PubMed and Google for AIM sets, here are 2 that I've looked at:

http://www.investigativegenetics.com/content/2/1/1

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649128/

Depending on what format your data is in, it should be pretty easy to do LD analysis yourself if you can't find an appropriate list of AIMs.

[vlaufer]

Hi Katie! Greetings from across the pond.

Been working on this a lot today. I think I'll do the LD analysis using Haploview as you suggest, however there are lists of continent specific markers. The best compendium I have found so far is http://genetics.med.harvard.edu/reich/Reich_Lab/Datasets.html

[Katie D'Aco]

Great resource, thanks for sharing