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how do i upload ancient dna on gedmatch

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  • how do i upload ancient dna on gedmatch

    about a week a ago on a thread at anthrogenica, i was told about some ancient dna from the pericues and 2 tamahuara mummies.
    http://www.anthrogenica.com/showthre...l=1#post102207

    yesterday night and this morning, i went through the trouble of using the bam analysis kit on the first listed pericues sample on the link above
    http://www.y-str.org/2014/04/bam-analysis-kit.html


    you can find the output files here
    https://drive.google.com/folderview?...1k&usp=sharing

  • #2
    It's not going to work as it is. Chromosomes 1 through 14 seem to be missing and the autosomal results file is only 14KB which is less than 1/10th the size of a 23andme file.

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    • #3
      Originally posted by Armando View Post
      It's not going to work as it is. Chromosomes 1 through 14 seem to be missing and the autosomal results file is only 14KB which is less than 1/10th the size of a 23andme file.
      huh aren't bam chromsomes parts 1-14 there on google docs links. also i admit i did this in two sessions since my laptop crasshed(since windows 10 is glitchy), maybe that's why that file was glitchy for you.

      maybe i'll try it again later on my dad's computer.

      also here's my attempt at doing the first tamahuara sample
      https://drive.google.com/folderview?...Xc&usp=sharing

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      • #4
        Originally posted by crossover View Post
        huh aren't bam chromsomes parts 1-14 there on google docs links. also i admit i did this in two sessions since my laptop crasshed(since windows 10 is glitchy), maybe that's why that file was glitchy for you.

        maybe i'll try it again later on my dad's computer.

        also here's my attempt at doing the first tamahuara sample
        https://drive.google.com/folderview?...Xc&usp=sharing
        For the Pericue sample chromsomes 1-14 are not in the autosomal file. I wouldn't have said that if they were there. You need to look at the filtered-autosomal-o37-results.csv.gz file. The file is glitchy just for me. It is just plain incomplete.

        Compare it to the Tarahumara file which has all of the chromosomes and is 122KB in size.
        Last edited by Armando; 20 August 2015, 09:28 PM.

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        • #5
          Originally posted by Armando View Post
          For the Pericue sample chromsomes 1-14 are not in the autosomal file. I wouldn't have said that if they were there. You need to look at the filtered-autosomal-o37-results.csv.gz file. The file is glitchy just for me. It is just plain incomplete.

          Compare it to the Tarahumara file which has all of the chromosomes and is 122KB in size.
          yeah i'm thinking the fact my computer crashed may have something to do with that. i'm gonna try to re-process that whole file again and replacing the current files with the updated ones

          also how would i upload the tamahuara file to gedmatch since gedmatch only give an ancestrydna,ftdna, and 23andme raw dna upload options.
          Last edited by crossover; 20 August 2015, 09:34 PM.

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          • #6
            Felix Immanual has a lot of experience in this and may be able to help.

            See

            http://www.y-str.org/

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            • #7
              Originally posted by Earl Davis View Post
              Felix Immanual has a lot of experience in this and may be able to help.

              See

              http://www.y-str.org/
              He had already replied in her thread at http://www.anthrogenica.com/showthre...ent-studies-on

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              • #8
                Originally posted by Armando View Post
                He had already replied in her thread at http://www.anthrogenica.com/showthre...ent-studies-on
                Thanks. I had missed that thread.

                Earl.

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