DIY admixture analysis

By Razib Khan | July 27, 2011 11:24 am

Dienekes Pontikos has just released DIY Dodecad, a DIY admixture analysis program. You can download the files yourself. It runs on both Linux and Windows. Since I already have tools in Linux I decided to try out the Windows version, and it seems to work fine. It is somewhat limited in that you start out with the parameters which Dienekes has set for you, but if you don’t want to write your own scripts and get familiar with all the scientific programs out there, I think this is a very good option. Additionally, it seems to run rather fast, so you won’t spend days experimenting with different parameters.

Dienekes has already run me, but I put my parents’ genotype files through the system. Here are the results:

Population Razib Mother Father
East_European 6.9 6.5 4.3
West_European 1.7 3.1 5.5
Mediterranean 6.3 5.6 5.9
Neo_African 0 0 0
West_Asian 0 2 3.9
South_Asian 65.9 59.6 60.4
Northeast_Asian 2.9 3.8 3.6
Southeast_Asian 15.8 16.6 15.5
East_African 0 0 0.2
Southwest_Asian 0.5 2.5 0.7
Northwest_African 0 0 0
Palaeo_African 0 0.3 0

The main thing to notice is that my mother has more total East Asian ancestry than my father, and, that she has a Southwest Asian component which is at a few percent. These are always consistent findings in the dozens of ADMIXTURE runs I’ve done with various parameter settings and reference population mixes, so it’s nice that DIY Dodecad replicates those findings. Though the population sets seem a bit Eurocentric to me, so I would recommend it most for those with West Eurasian ancestry.

  • Insightful

    Your mother’s West Asian is 2 and your father’s West Asian is 3.9 (almost 4), yet, you are zero?..

  • Ian

    It gave me ather different results from what I got from Zack’s analysis. For example, on HAP South Asian + Onge was 42%, while DIYDodecad only showed me as 28% South Asian. Others were more similar – HAP showed me as 13% Southwest Asian, while Dodecad’s West Asian (9.77%) + Southwest Asian (2.94%) was 12.71%.

    Dodecad seems to think I am a lot more East Asian than does either HAP or 23andme. 23andme says 4% Asian. HAP says 2% East Asian, 1% Siberian. Dodecad, on the other hand, says 0.93% Northeast Asian and 5.80% Southeast Asian. That’s 7% – about twice what the others say.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Your mother’s West Asian is 2 and your father’s West Asian is 3.9 (almost 4), yet, you are zero?..

    i already covered why this might be a real result and might not just noise extensively.

    http://blogs.discovermagazine.com/gnxp/2011/01/asian-in-all-the-right-places/

    but for DIY Dodecad it might be noise too. this should be used as a first pass i think.

    #2, he doesn’t have a south asian skewed reference set like zack. some of the ASI is padding your east asian. i’m probably 5-10% east asian, but dodecad is giving be 15%.

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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