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Kids' results minus Mom = deceased Dad?

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  • #16
    The raw data files I have from FT-DNA are in the form "filename.csv.gz" I copied one and renamed it DUMMY. Finally got it unzipped. By default, it opens in Excel, which makes it easier to replace G, A, T, and C with "-" (without having to worry about the RSIDs). I will copy and save to txt file. (Is this right?)

    BUT... I only see records for chromosomes 1 and 2. There should be 22 (or 23?), shouldn't there? When I opened the file, I got a message saying the file didn't open completely. I'm thinking it isn't all there... even though there are over 65K records.

    Kathy

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    • #17
      How to unzip .gz files.

      Since WinRAR is a payware, as an alternative on Windows one can use free 7-ZipW.

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      • #18
        Thanks. Unzipping is done. Trying to make friends with Mr. Pike's program right now. First run didn't look right.

        I have mom's and 2 children. First run gives only question marks for dad's.

        Not quite sure what I'm doing wrong.

        k.

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        • #19
          Originally posted by GoofusBroadway View Post
          Thanks. Unzipping is done. Trying to make friends with Mr. Pike's program right now. First run didn't look right.

          I have mom's and 2 children. First run gives only question marks for dad's.

          Not quite sure what I'm doing wrong.

          k.
          The column labelled Father will be all Question marks as that column represents the dummy file which is all no calls.

          The very last columns labelled O+, is the Data the program separated out as your fathers possible values.

          below is what each column represents from David Pikes webpage.

          SNP data (the chromosome number, the SNP's name, and the SNP's position)
          the raw unphased data for the mother
          the raw unphased data for the father
          for each child:
          the child's raw data (either phased or unphased)
          the allele inherited from the mother
          the allele inherited from the father
          the allele from the mother that was not inherited by the child
          the allele from the father that was not inherited by the child
          two pattern sequences, the first being the overall pattern of inherited alleles from the mother, and the second being the overall pattern of inheritance of alleles from the father.
          two alleles from the mother, phased so that each column represents one of the mother's two chromosomes
          two alleles from the father, phased so that each column represents one of the father's two chromosomes

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          • #20
            I'm following this post to see how it rolls for all of you. This is something I've been hoping to see ever since I joined GEDmatch a couple of years ago. With the Tier 1 membership at GEDmatch, there is a tool called Lazarus that is supposed to do this, but my attempts at creating it with my 2 sisters and I plus our mother were unsuccessful at creating what appeared to be an accurate representation. (i.e., running the dummy kit back against the siblings created an MRCA of 2.0 rather than 1.0 as it should be).

            The living spouse file was optional (which seemed odd to me since that would appear to be the best way to phase the deceased parent's data from the children's files) but it instead relies on aunts, uncles, cousins, in the 2nd group to create the dummy kit. Without a lot of identified 2nd group relatives, one would have to run an NICW with the living spouse to get enough data to create a file that meant anything. Of course, that would risk a potential problem of introducing IBS segments into the mix unless one had a large number of identified matches. Either way, multiple runs of dummy kits weren't quite to my satisfaction.

            Anyway, as you all work through this and after my work schedule frees up, I'll give it a go as well.

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