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Thread: How can I calculate admixtures in one chromosomal segment on Gedmatch?

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    How can I calculate admixtures in one chromosomal segment on Gedmatch?

    Is it possible to separate one segment and see percentages of genetic admixtures in it and then see by oracle results on Gedmatch for example to which population it is closer to?
    23andme: 86,8% Eastern European, 9,1% Greek and Balkan, 1,2% Western Asian, 0,7% Ashkenazi Jewish, 0,3% Spanish and Portuguese, 1,4% Broadly Southern European, 0,5% Broadly European

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    On Gedmatch, the smallest segment you can calculate is a single chromosome. You could then use the Oracle utilities offline described in this thread to run those percentages against the population reference spreadsheets:

    https://anthrogenica.com/showthread....ll=1#post95003

    If you want to run a section or segment of one chromosome, you would first have to run DIYDodecad in "target" mode where you pick a chromosome and a start/stop location to get the admixture percentages. Then, you could run those with the Oracle utilities. An alternative is to just run your segment using a high K calculator, like Eurogenes K36, and then an Oracle may not be as important because the admixture percentages already become more regional in nature. You can see examples of me doing that here:

    https://anthrogenica.com/showthread....l=1#post165530

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    Quote Originally Posted by randwulf View Post
    On Gedmatch, the smallest segment you can calculate is a single chromosome. You could then use the Oracle utilities offline described in this thread to run those percentages against the population reference spreadsheets:

    https://anthrogenica.com/showthread....ll=1#post95003

    If you want to run a section or segment of one chromosome, you would first have to run DIYDodecad in "target" mode where you pick a chromosome and a start/stop location to get the admixture percentages. Then, you could run those with the Oracle utilities. An alternative is to just run your segment using a high K calculator, like Eurogenes K36, and then an Oracle may not be as important because the admixture percentages already become more regional in nature. You can see examples of me doing that here:

    https://anthrogenica.com/showthread....l=1#post165530
    Do you know how to look in wich copy of the chromosome 20 it is. The copy 1 or the copy 2?

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    Quote Originally Posted by chrisbab View Post
    Do you know how to look in wich copy of the chromosome 20 it is. The copy 1 or the copy 2?
    That is a little more difficult. With admixture output, you don't really get that as an output. One user here for a short time had an analysis that was broken out that way, but the test wouldn't be available anymore. Here is a thread I started on that one:

    https://anthrogenica.com/showthread....l=1#post225969

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    Quote Originally Posted by randwulf View Post
    That is a little more difficult. With admixture output, you don't really get that as an output. One user here for a short time had an analysis that was broken out that way, but the test wouldn't be available anymore. Here is a thread I started on that one:

    https://anthrogenica.com/showthread....l=1#post225969
    Why it is more dificult to do that on admixture studio?How they easily do that on 23andme chromosome painting? This is so retarded there should be an option for that. I want to know from which side of the parent comes the copy of the cromosome. Even it it is more difficult to do that is there a way to do that?

    By the way, i found that: https://dnagenics.com/how-to-analyze...ixture-studio/ But how do i follow thoses instructions?
    Last edited by chrisbab; 01-12-2021 at 11:53 PM.

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    Quote Originally Posted by chrisbab View Post
    Why it is more dificult to do that on admixture studio?How they easily do that on 23andme chromosome painting? This is so retarded there should be an option for that. I want to know from which side of the parent comes the copy of the cromosome. Even it it is more difficult to do that is there a way to do that?

    By the way, i found that: https://dnagenics.com/how-to-analyze...ixture-studio/ But how do i follow thoses instructions?
    Yes, there may be other tools than admixture that can be helpful. You can do the phasing on Gedmatch and that does split your kit into two based on parents. Then you can run admixture on the split kits, but the results can look a little odd.

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    Quote Originally Posted by randwulf View Post
    Yes, there may be other tools than admixture that can be helpful. You can do the phasing on Gedmatch and that does split your kit into two based on parents. Then you can run admixture on the split kits, but the results can look a little odd.
    Can i do that if i do not have yet my parents kits?

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    You must have at least one parent kit for it to do the split.

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