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Compare two sets of Geno 2.0 raw data?

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  • Compare two sets of Geno 2.0 raw data?

    Hi all,

    Are there any third-party sites/software out there that would be able to read two Geno 2.0 results and determine the degree of genetic relationship?

    Thank you in advance for any help.

  • #2
    Originally posted by e-burger View Post
    Hi all,

    Are there any third-party sites/software out there that would be able to read two Geno 2.0 results and determine the degree of genetic relationship?

    Thank you in advance for any help.
    You can use David Pike's utility to compare two files. Since the number of SNPs is smaller, I'd suggest reducing the default SNP threshold to say 200 and see how things fall out.

    http://www.math.mun.ca/~dapike/FF23utils/pair-comp.php

    When I ran my son's Geno 2.0 file against some 23andMe results for known second cousins, the shared segments were easily detectable. However, you are likely to end up with some false positives, especially for more distant relatives, and if the match is important, I'd recommend retesting with a standard autosomal test to see if results hold up with more SNPs.

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    • #3
      Does this utility accept Geno files? For some reason FTDNA won't display an option to download raw data for one of the persons, despite having transferred the Geno kit and displaying FTDNA results.

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      • #4
        Originally posted by e-burger View Post
        Does this utility accept Geno files? For some reason FTDNA won't display an option to download raw data for one of the persons, despite having transferred the Geno kit and displaying FTDNA results.
        You would need to get the raw autosomal data from the Genographic site. The transfer process just covers Y and mtDNA haplogroup information. I'm away from home right now, so I don't have access to all my files. I have a vague recollection that I did need to tweak the format a bit to work with Pike's utilities, but it was easy enough to do in Excel.

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        • #5
          Thanks! Does Dr. Pike provide any documentation to guide how to interpret the results? There don't seem to be any links on this page or his other pages.

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          • #6
            Originally posted by e-burger View Post
            Thanks! Does Dr. Pike provide any documentation to guide how to interpret the results? There don't seem to be any links on this page or his other pages.
            No, it's purely a calculator for matching segments, so it's more of a screening tool. It also uses megabases (Mb) instead of cM. You would need to have some feel for what to expect in terms of number and size of matching segments and look up the cM values if you want to follow up on anything that looks interesting.

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            • #7
              Makes sense. Would you be able to refer to appropriate literature to go to, armed with Dr. Pike's results?

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              • #8
                Originally posted by e-burger View Post
                Makes sense. Would you be able to refer to appropriate literature to go to, armed with Dr. Pike's results?
                Blaine Bettinger's "Shared cM Project" would be my first stop.

                http://www.thegeneticgenealogist.com...ed-cm-project/

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                • #9
                  Thanks. Still hard to comprehend to a layperson

                  Is it safe to assume that several matches thousands-long on Chr Y imply paternal line relation/ancentry?

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                  • #10
                    Originally posted by e-burger View Post
                    Thanks. Still hard to comprehend to a layperson

                    Is it safe to assume that several matches thousands-long on Chr Y imply paternal line relation/ancentry?
                    Most males will match on many/most Y chromosome markers in the Geno 2.0 They are used to assign your haplogroup. Only an exact match would be of any interest, and even then, the common ancestor could have lived thousands of years ago.

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                    • #11
                      I was wondering if this thread was going to turn into a Y-DNA question.

                      You need to get a Y-DNA37, Y-DNA67, or Y-DNA111 STR test to find people that are potentially closely related in the direct paternal line. If those matches also had a Geno 2.0 test or also have done extensive Y-DNA SNP testing and they belong to a branch that diverged from yours 2,000 years ago or more then you don't have a common Y-DNA ancestor with them in that time frame. If they haven't had a Geno 2.0 or extensive SNP testing you would have to ask them to do that even if they are a Y-DNA37 or Y-DNA67 match.

                      What is the terminal Y-DNA SNP that Geno 2.0 gave you?

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                      • #12
                        Originally posted by Armando View Post
                        I was wondering if this thread was going to turn into a Y-DNA question.
                        Only because Dr. Pike's tool returned extensive matches along the Y chromosome and not others.

                        What is the terminal Y-DNA SNP that Geno 2.0 gave you?
                        Z99 in both cases.

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                        • #13
                          Originally posted by e-burger View Post
                          Only because Dr. Pike's tool returned extensive matches along the Y chromosome and not others
                          I see.

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                          • #14
                            How scientific is it to dump the two Geno data sets into a database, create a query joining on SNP codes, and compare allele matches vs. non-matches to see what percentage the matches approach?

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