Question: How To Extract Snp From Wga Data, Responsible For A Specific Ancestry In Admixture Plot
1
gravatar for User 0422
8.0 years ago by
User 0422150
User 0422150 wrote:

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

• 1.7k views
ADD COMMENTlink modified 7.6 years ago by Larry_Parnell16k • written 8.0 years ago by User 0422150
1
gravatar for Larry_Parnell
7.9 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 7.9 years ago by Larry_Parnell16k
0
gravatar for Jorge Amigo
8.0 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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".

ADD COMMENTlink modified 8.0 years ago • written 8.0 years ago by Jorge Amigo11k
1

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

ADD REPLYlink written 7.9 years ago by User 0422150
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