How To Extract Snp From Wga Data, Responsible For A Specific Ancestry In Admixture Plot

Question

[User 0422]

Hi all,

When we run ADMIXTURE plot we get different ancestry components among different populations. Let's say if I want to extract specific SNPs responsible for specific ancestry component in all the populations. Is there a way to do so?

Any help will be highly appreciated.

thanks

Answer 1

[Larry_Parnell]

We use STRUCTURE, which is very similar to ADMIXTURE, but we have not tried to extract the SNPs driving the ancestry components because to date we have preferred to look at the total result. Nonetheless, it should be a simple part of the ancestry output where the contribution of each SNP is given.

Answer 2

[Jorge Amigo]

this paper may help you:

Ralph E. McGinnis, Visualizing Chromosome Mosaicism and Detecting Ethnic Outliers by the Method of “Rare” Heterozygotes and Homozygotes (RHH) , Human Molecular Genetics, 2010, Vol. 19, No. 13 2539–2553, doi:10.1093/hmg/ddq102

I'm not an expert on the field, but I saw it referred on an interesting blog entry where the author presented a worked example to detect in fact "ethnic outliers".

[User 0422]

I am sorry but that is not helpful. thanks anyway.