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Use of Geno2.0 in Gedmatch

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  • Use of Geno2.0 in Gedmatch

    This thread of three postings from John Walden (at last count) treat with the utility of GenoChip data for cousin matching in Gedmatch and relative performance of GenoChip compared to other datasets.

    http://archiver.rootsweb.ancestry.co...-12/1355705497

  • #2
    Use of Geno 2.0 in Gedmatch

    Has anyone else uploaded their Geno 2.0 data to Gedmatch? Any problems or tricks to making it work? Did you enter a new kit number and if so how did you identify your new file?

    Jim

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    • #3
      Use of Geno 2.0 in Gedmatch

      Just tried to upload, but without success. Got this error message:

      ERROR: Line segmentation count = 6
      Each line of data must consist of 4 values

      Line: gsgt version 1.9.4

      Any hints welcome.

      Jim

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      • #4
        Contact Gedmatch admin John Olson or John Walden.

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        • #5
          I don't see a link at Gedmatch dedicated to uploading GENO results... Am I missing something?

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          • #6
            Use of Geno 2.0 in Gedmatch

            Originally posted by tomcat View Post
            Contact Gedmatch admin John Olson or John Walden.
            Do you have email addresses for them? Can't find any on the site.

            Jim

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            • #7
              Status of Geno2.0 uploads to GEDmatch

              John Walden made extensive changes to the Geno2.0 data format to make it work on GEDmatch. It also required manual changes to the GEDmatch database on my part. This kind of research is needed to determine what evaluation thresholds are appropriate for this kind of data. It also confirms the level of confidence in comparisons and Ad-mix results.

              The Geno2.0 files are not uploadable to GEDmatch in their present form. I was not planning on making Geno2.0 upload capability available, but if there's enough interest, I may reconsider. Even so, my time is quite limited for the forseeable future, so I'm not sure how long it would take.

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              • #8
                Originally posted by JOlson View Post
                John Walden made extensive changes to the Geno2.0 data format to make it work on GEDmatch. It also required manual changes to the GEDmatch database on my part. This kind of research is needed to determine what evaluation thresholds are appropriate for this kind of data. It also confirms the level of confidence in comparisons and Ad-mix results.

                The Geno2.0 files are not uploadable to GEDmatch in their present form. I was not planning on making Geno2.0 upload capability available, but if there's enough interest, I may reconsider. Even so, my time is quite limited for the forseeable future, so I'm not sure how long it would take.
                Thanks; looks like it might be interesting at some point but not a priority.

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                • #9
                  So, the Geno 2.0 dataset performs fairly well for cousin matching but not as well as the denser datasets such as from 23&Me (or FTDNA?). But simply comparing one dataset performance to another is not all that interesting. What would be interesting, and a fair test of all datasets, is to interleave or collate all datasets into one, where the coverage of one fills-in the gaps of another and then run comparisons of performance in ancestry admixture and cousin matching between collated results and un-collated results.

                  There are more than a few participants in this area that have tested with all four test providers.
                  Last edited by tomcat; 18 December 2012, 11:53 PM.

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                  • #10
                    Originally posted by JOlson View Post
                    John Walden made extensive changes to the Geno2.0 data format to make it work on GEDmatch. It also required manual changes to the GEDmatch database on my part. This kind of research is needed to determine what evaluation thresholds are appropriate for this kind of data. It also confirms the level of confidence in comparisons and Ad-mix results.

                    The Geno2.0 files are not uploadable to GEDmatch in their present form. I was not planning on making Geno2.0 upload capability available, but if there's enough interest, I may reconsider. Even so, my time is quite limited for the forseeable future, so I'm not sure how long it would take.
                    I would love to see a geno2 calculator on GedMatch.

                    Comment


                    • #11
                      Originally posted by Andiralenira View Post
                      I would love to see a geno2 calculator on GedMatch.
                      Ditto.

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                      • #12
                        Gedmatch

                        I also hope Gedmatch will one day make Geno 2.0 upload possible.

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