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View Poll Results: What do you think about ADMIXTURE?

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  • It is the future of ancestry analysis

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  • It seems a bit dodgy

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  • I can make it work, just let me have a go!

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Thread: Admixtures

  1. #1
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    Admixtures



    Latest version of Admixture http://www.genetics.ucla.edu/softwar.../download.html

    ADMIXTURE is a computer software program that once calibrated by a knowledgeable tutor, is used to estimate an individual's ancestral composition by analyzing the allele frequencies from autosomal SNP data.

    The ADMIXTURE program is used to estimate the number of underlying populations through a process of cross-correlation experiments. To do this, individuals of known ancestry are exploited to yield more precise ancestry estimates.

    Once ancestral components have been uncovered, small admixture coefficients are eradicated for each individual, encouraging model parsimony and often yielding more interpretable results for small data-sets or data-sets with dissimilar populations.
    BMC Bioinformatics 2011, 12:246doi:10.1186/1471-2105-12-246

    ADMIXTURE is currently the platform used by most hobbyists and amateur population geneticists.

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    1 out of 1 members found this post helpful.
    Here are the free tools available for calculating admixture percentages using 23andMe, FTDNA and deCODEme genotype data.

    Using the Do-It-Yourself Dodecad v 2.1 that you can find here [includes the Dodecad v3 calculator files]

    You are able to calculate your autosomal admixture percentages using the following calculators:

    Download the Dodecad v3 calculator here
    Download the Euro7 calculator by Dodecad here
    Download the BAT calculator by Dodecad here
    Download the weac calculator by Dodecad here
    Download the Africa9 calculator by Dodecad here
    Download the Eurasia7 calculator by Dodecad here
    Download the Euro-DNA-Calc111 calculator by Dodecad here
    Download the Eurogenes Eurasian K=10 by Davidski here
    Download the Eurogenes K=14 by Davidski here
    Download the MDLP K=7 by Vadim Verenich here

    Download the Dodecad Oracle v1 calculator here

    The Dodecad Oracle v1 tool allows you to view your closest population matches and for those with unknown mixed ancestry it lists mixed population matches.

    Dodecad software is provided free of charge for non-commercial use by Dienekes Pontikos @ http://dodecad.blogspot.com

    If you are having trouble using the program I would be happy to help if I can.
    Last edited by Dorianfinder; 08-11-11 at 18:32.

  3. #3
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    You should add the recent Eurasia7, if you check the post you'll see there's also a Calculator for it (several individuals were not included).

    Also, there was a Calculator for the Eurogenes K=14, but Davidski removed the post. I don't know if the link is available somewhere, but I have the ZIP. If someone wants to calculate it, I could upload the file. I think it's better than the K=10 in some aspects.

    Another interesting point, is that I recently wrote to Dienekes' proposing him to provide tools for the calculation of samples from data source (HGDP, Behar, etc.) using DIY. That will allow people to compare personal results, not only with known people joining the projects, also with those anonimous individuals whose results are only visible sometimes in the population portraits (Dodecad v3) and the Eurogenes project. Just note in the Euro7, Eurasia7, Weac, etc., they are listed as average, but not individually. Then, if Dienekes' finally finds the way to convert this files into a compatible format for DIY, we could see exactly their admixture proportions in the different tests.

    For the moment he is busy and told me it can't be done easily, but I'm sure he'll try to do so :)

  4. #4
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    The Eurasia7 by Dodecad and the Eurogenes K=14 by Davidski have been added to the list.
    Last edited by Dorianfinder; 07-11-11 at 00:06.

  5. #5
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    I uploaded the K=14 here: https://docs.google.com/open?id=0B8-...JmM2Y5YTNiNzA0

    You can list the link together with the others, Dorian.

    The components are:
    - Northeast Euro (peaks in Russians)
    - West Euro (Basques & Irish)
    - East Mediterranean (Cypriots)
    - Volga-Ural (Chuvashs)
    - West Asian (Lezgins)
    - Middle Eastern (Saudis)
    - Berber (Mozabite Berbers)
    - South Asian (South Indians)
    - North Asian (Nganassans)
    - South Siberian (Evenks)
    - East Siberian (Koryaks)
    - East Asian (Japanese)
    - Southeast Asian (Southern Chinese)
    - Sub-Saharan (Western Africans)

    Enjoy!

    UPDATE: To run the K=14 the word "test" instead "dv3" is required. That's all.
    Last edited by Knovas; 07-11-11 at 02:34.

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    I also uploaded the last version of the Euro-DNA-Calc here: https://docs.google.com/open?id=0B8-...ZjZjg0NjY1ZTBl

    It can be added at the beggining too :)

    Components:
    - Northwest Euro
    - Southeast Euro
    - Ashkenazi Jewish

    It's very simple and must be taken with caution, since sometimes the reports don't make any sense. Keep in mind that Northwest Euro can include plain Western European allele frequencies (I know that because I got 75% there being Iberian), and having some West Asian admixture could report Ashkenazi Jewish here. Just this, be carefull with the interpretations, and pay attention to the major percents.

  7. #7
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    Thanks! The Euro-DNA-Calc software is compatible with 23andMe and deCODEme genotype data whereas the other calculators found in the list in post #2 are all compatible with FTDNA, 23andMe and deCODEme genotype data.
    Last edited by Dorianfinder; 08-11-11 at 18:33.

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    Quote Originally Posted by Dorianfinder View Post
    calculate your autosomal admixture percentages using the following calculators
    Thank you very much for this useful list/links and thread; also Knovas for his additions.

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    1 out of 1 members found this post helpful.

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    ADVANCED ANALYSIS

    All 22 chromosomes can be analyzed using the 'bychr' mode instead of the 'genomewide' mode in the dv3.par file found in all dodecad calculators mentioned above. Similarly, ancestry percentages for individual segments of an individual's genome can be calculated using the 'byseg' mode.

    The accuracy of analysis increases when viewing all 22 chromosomes. Also, one can study the individual chromosomes and create a graphic representation of each chromosome's ancestral admixture.

    If you have used this software please feel free to post your experience here.
    Last edited by Dorianfinder; 23-11-11 at 21:18.

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    Lightbulb SNP Map

    SNP Map

    This tool allows you to browse your individual snp frequencies, and allows you to compare your particular snp to its frequency within other population groups.

    The program is downloaded onto your pc and you upload your raw data files from either Relative Finder or Family Finder onto the program. It's user-interface is a no-frills database but it does the job well. It allows you to analyze your individual snps with full confidentiality and it's free.

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    I already checked it quickly with different raw data's from people I know: 1 mixed Iberian (different regions), 1 mostly Catalan (me) a Basque individual and an Angloamerican of mostly English/Irish descent.

    I looked at Chromosome X in all cases to see it under similar conditions, and it basically shows there's apreciable shared ancestry between populations. Not all markers are informative in ancestral terms, some of them are related to health or something like this, but I'm not a professional to distinguish them. However, I did not see huge differences between this 4 individuals, it's not rare for example to find a genotype present in 90% of African population and, lets say, only 20% in Europe. At least, I could apreciate it in all the individuals, but perhaps the "sample size" it's too low.

    Well, there are a lot of markers one could check with different interpretations. There's nothing more I could say considering my knowledge, just some observations. Other people much versed in allele frequencies would be of greater help.

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    Quote Originally Posted by Knovas View Post
    I did not see huge differences between this 4 individuals, it's not rare for example to find a genotype present in 90% of African population and, lets say, only 20% in Europe. At least, I could apreciate it in all the individuals, but perhaps the "sample size" it's too low.
    The 20% found in Europe and Africa refers to shared admixture (convergence). If you want to decrease this overlap you can increase reliability from 80% to 95%. The Relative Finder X-chromosome data file has many non-ancestral markers, unlike the FTDNA Family Finder data file which is ancestral in its entirety.

    Allele frequencies can be considered reliable when a particular admixture component is found in progressive strands spanning more than 1mil, if it's unbroken over 6mil then ancestry is certain.

    Many people don't know what to do with the X-chromosome data file they get from RF and FF. In fact, it's much better than an mtdna test and the best indication of maternal ancestry. The X-chromosome is passed onto men by their mothers and includes all maternal great-grandmothers, so it's amazingly useful for individuals from the USA and South Africa who think they may have a great-grandmother who may have had possible Amerindian or slave ancestry.

    X-chromosome pedigree chart.png

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    Thanks. All the raw data's I checked are from 23andme, which of course have many non ancestral markers. Anyways, I'll consider your suggestions and continue exploring similarities.

    I think the idea of the program it's quite good, and it could be helpfull for the design of new analysis. Possibly both Dienekes' and Davidski used it for something.

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    Lightbulb New Dodecad Tools

    Download the K12a calculator here
    Download the world9 calculator here

    Download the Dodecad Oracle (K12a version) here (left click 'file' to download)
    Last edited by Dorianfinder; 20-12-11 at 12:03.

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    Thanks Dorian, I was about to miss the World9. Interesting this one, I'm going to start a thread for comparison with the previous Eurasia7.

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    Help with the program

    Hello,

    Could someone please tell me how to use the the Dodecad program for windows, it's says unzip your file to a working directory, I don't get what it is talking about, I just can't seem to get the program to work, could someone give me some instructions that are easy to understand.


    Thank you
    aaliy06

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    You must create a new folder and call it "working directory", that's what it means. Then, extract the analysis components into this one and continue following the instructions. You need to add the DIY archive and your transformed genotype data (in a format understood by DIY).

    Note that previously you must download the latest version of DIY and the R program. I'm assuming you did.

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    Yes I downloaded the latest version, does it matter where you put the working directory folder at? I mean can you put it in your documents or does it have to be on your C: drive? and do you have to have the quotation marks?

    Thanks
    aaliy06

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    One more thing, what is the format that DIY understands?

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    I think it doesn't matter where you create the folder. If it doesn't work, just change the position. Mine are in my documents (I have many working directories for the different calculators) and there's no problem.

    The format that DIY understands is the transformation you'll have to do on your raw data following the instructions. Unzip your data inside the working directory, follow the preliminary steps, and an archive called "genotype" will emerge inside the working directory. This one will be valid for all calculators designed for DIY; the only one which DIY is able to read and extract admixture proportions.

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    Guys you are fired.Let's see, a rookie, for example from Europe like me, what is the best calculator to start and which in turn give spectacular results, clear and easy to understand? otherwise we will end up in a mental hospital all.

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    Lightbulb

    Quote Originally Posted by aaliy06 View Post
    Hello, Could someone please tell me how to use the the Dodecad program for windows, it's says unzip your file to a working directory, I don't get what it is talking about, I just can't seem to get the program to work, could someone give me some instructions that are easy to understand. Thank you aaliy06
    If you need to unzip any files you can download this user-friendly software here. Just install and drag any zipped files over it to have them uncompressed. Go to documents in windows and create a file named DIYDOD. Save all your admixture calculator files in this folder. Then save your 23andme or ftdna data file to this folder. Everything should be in the same file location, namely the file that you created, named DIYDOD, in windows documents. You need to download the R console software here. You will enter your commands into this console once you have installed it. Now you are ready to enter the following four commands: setwd('DIYDOD') This command tells the program where to look for all the files, namely the DIYDOD file created in windows Documents. source('standardize.r') This command standardizes the data preparing it for the analysis. standardize('???.csv', company='ftdna') This command tells the program the name of your data file and the company where you tested. system('DIYDodecadWin dv3.par') This is the final command. Wait a few minutes for your admixture results to appear. If in future you would like to use a different calculator just add the new calculator's name in place of dv3 (eg. euro7) and download the (eg. euro7) files to your DIYDOD file in documents. Your final command for the different calculators will look like this: system('DIYDodecadWin euro7.par') For the Euro7 calculator. system('DIYDodecadWin eurasia7.par') For the Eurasia7 calculator. system('DIYDodecadWin africa9.par') For the Africa9 calculator.

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    Thank you, I will give it a try

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    Quote Originally Posted by Carlos View Post
    Guys you are fired.Let's see, a rookie, for example from Europe like me, what is the best calculator to start and which in turn give spectacular results, clear and easy to understand? otherwise we will end up in a mental hospital all.
    Try the K=12v3 and the Euro7 to get an aproximate idea if you don't want to run all tests. This is the easiest thing to understand.

    However, I must mention the K12a, which is the latest experiment and the data Dienekes' is currently using. In my opinion is not the same clear, but for comparison with other people of similar ethnic background it's okay.

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    Hello,

    I finally got it to work, so thank you so much for helping me, now I would like to know how you use the byseg and the bychr? if someone can help me on that.

    Thank you

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