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Kids' results minus Mom = deceased Dad?

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  • Kids' results minus Mom = deceased Dad?

    I have all three of us kids' FF results now -- and Mom's. Dad died in 1988, so there will not be any results for him.

    Is there a way to subtract Mom's results from those of us kids combined in order to get a sort of notion of what Dad's autosomal results might look like?

  • #2
    Try gedmatch.com. They have functionality for phasing and for predicting the DNA of a deceased parent.

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    • #3
      For a more advanced option there is also a David Pike Utility that will phase out your fathers values and build his DNA profile.
      With 3 children and a spouse you should be able to determine around 85% to 95%
      It is a multi step process which initially requires you to create a "dummy" file of no calls for missing parent to run utility.

      http://www.math.mun.ca/~dapike/FF23u...bs-2parent.php

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      • #4
        Wow, that is great news; thanks!

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        • #5
          Looks like Mr. Pike's utilities are still available. How does one create a "dummy file" to use for the missing parent?

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          • #6
            Originally posted by GoofusBroadway View Post
            Looks like Mr. Pike's utilities are still available. How does one create a "dummy file" to use for the missing parent?
            open your raw data with notepad, hit CTRL+H (if using programmers notepad then hit CTRL+F and click on Replace)

            in Find What enter A
            in Replace with enter -

            Click on Replace All

            Repeat with the letters C, T, and G

            end result will look like the following
            "rs3094315","1","742429","--"
            "rs3131972","1","742584","--"
            "rs12562034","1","758311","--"
            ect.....

            Save file under different name as either a .txt or .csv

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            • #7
              Originally posted by prairielad View Post

              ...........

              end result will look like the following
              "rs3094315","1","742429","--"
              "rs3131972","1","742584","--"
              "rs12562034","1","758311","--"
              ect.....

              Save file under different name as either a .txt or .csv
              should clarify the difference if using 23andme Raw Data (.txt) or FTDNA Raw Data (.csv) files.

              Above is how FTDNA's .csv file will look

              23andme's .txt file will look more like this

              rs4477212 1 82154 --
              rs3094315 1 752566 --
              rs3131972 1 752721 --
              rs12124819 1 776546 --
              rs11240777 1 798959 --

              Words in file containing these letters will have these letters replaced, but it does not effect the file so don't worry about the wording being messed up.....
              Last edited by prairielad; 27 December 2014, 06:22 PM.

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              • #8
                Originally posted by prairielad View Post
                For a more advanced option there is also a David Pike Utility that will phase out your fathers values and build his DNA profile.
                With 3 children and a spouse you should be able to determine around 85% to 95%
                It is a multi step process which initially requires you to create a "dummy" file of no calls for missing parent to run utility.

                http://www.math.mun.ca/~dapike/FF23u...bs-2parent.php
                Is it possible to reconstruct the DNA of the father with only 2 siblings and the mother, or are 3 needed?

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                • #9
                  Originally posted by bourgja View Post
                  Is it possible to reconstruct the DNA of the father with only 2 siblings and the mother, or are 3 needed?
                  On average, for the total DNA of a parent (maternal and paternal chromosomes)to be passed on to children, they have to have 4 children.

                  You can build a DNA profile of missing parent from results of only 1 child and 1 parent. But these results will only consist of one value per position.
                  This is typically what one is doing when Phasing

                  ie
                  rs28391282 1 894028 G
                  rs2340592 1 900798G
                  rs13303118 1 908247 T

                  versus tested results

                  rs28391282 1 894028 GG
                  rs2340592 1 900798 AG
                  rs13303118 1 908247 TG

                  If there is only 1 child, then the most you can reconstruct is 50% of that parent.
                  Each position has two values(one from maternal chromosome and one from paternal chromosome), of which only one is passed on to child.

                  Adding each consecutive child into the results allows you to figure out that much more. Having multiple siblings (3+) tested just give you better odds at figuring out missing parents total DNA (maternal and paternal values) with better accuracy.

                  Think of it this way
                  Siblings will share with each other as follows depending on which single chromosome section they received from each parent (maternal or paternal chromosome).
                  ie)
                  received segment of mothers maternal chromosome, it will be your maternal grandmothers DNA
                  received segment of mothers paternal chromosome, it will be your maternal grandfathers DNA
                  received segment of fathers maternal chromosome, it will be your paternal grandmothers DNA
                  received segment of father paternal chromosome, it will be your paternal grandfathers DNA

                  Full Siblings will match one another in one of the following 3 ways.
                  1)same maternal grandparent and same paternal grandparent (Full identical)
                  2)share same maternal grandparent but inherited opposite paternal grandparents or share same paternal grandparent but inherited opposite maternal grandparent(half identical)
                  3)inherited opposite maternal grandparents and opposite paternal grandparents (no match)

                  With only two children, there will be segments where they will share the same grandparent (parent of missing parent) in which you will only be able to determine half the missing parents DNA (one value). Adding additional children, one just has better odds that one or more received opposite grandparents along each segment of DNA, enabling one to figure out both of maternal and paternal values of missing parents

                  Keep in mind there will always be some positions that can not be determined.
                  For example if mother is AG and each child is AG, there is no way of knowing what the fathers value will be as it will be either AA, AG, or GG.
                  Last edited by prairielad; 29 December 2014, 08:45 PM.

                  Comment


                  • #10
                    Originally posted by prairielad View Post
                    open your raw data with notepad, hit CTRL+H (if using programmers notepad then hit CTRL+F and click on Replace)

                    in Find What enter A
                    in Replace with enter -

                    Click on Replace All

                    Repeat with the letters C, T, and G

                    end result will look like the following
                    "rs3094315","1","742429","--"
                    "rs3131972","1","742584","--"
                    "rs12562034","1","758311","--"
                    ect.....

                    Save file under different name as either a .txt or .csv
                    Originally posted by prairielad View Post
                    should clarify the difference if using 23andme Raw Data (.txt) or FTDNA Raw Data (.csv) files.

                    Above is how FTDNA's .csv file will look

                    23andme's .txt file will look more like this

                    rs4477212 1 82154 --
                    rs3094315 1 752566 --
                    rs3131972 1 752721 --
                    rs12124819 1 776546 --
                    rs11240777 1 798959 --

                    Words in file containing these letters will have these letters replaced, but it does not effect the file so don't worry about the wording being messed up.....
                    Slight modification to my above posts on making a dummy file

                    There are some RSID's (at least in FTDNA raw data) labelled beginning with VG (ie VG01S1077)
                    Therefore when Replacing the G, it messes with this RSID's label and if not corrected these positions will be omitted from David Pikes results.

                    To Remedy, in Replace window do the following

                    in Find What enter V-
                    in Replace with enter VG

                    Click on Replace All
                    Last edited by prairielad; 29 December 2014, 10:57 PM.

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                    • #11
                      Ok, I'm at David Pike's link; I made a dummy file for Dad, entered Mom and the kids' zipped raw data files; and it's not working. It never finishes; just keeps trying.

                      Plus, it's one chromosome at a time. If I got results, would I just add each set of results to the last on a single document until I had them all?

                      At Gedmatch, the only phasing utility I see is two parents and a child. Not sure how I would get my dad's DNA set out of that.

                      Comment


                      • #12
                        files have to unzipped, and I believe, not positive, they have to be in the same format

                        as I mentioned it is a bit of work, have to do 1 chromosome at a time and build a file.

                        Phasing at Gedmatch will separate each siblings DNA into their maternal and paternal side. Each file will only be a maximium of 50% of each parent of which you can run admixtures on as well as one to many comparisons.

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                        • #13
                          Oh, yeah, he does say UNzipped; thanks. Gedmatch wanted them zipped.

                          Ok, assuming I do that; as I said, do you just add each following chromosome results to the same document to build the file? Are they text format?

                          And right, at Gedmatch I run each of us separately -- and then how do I proceed, please, to add them together? Is that "admixture?" Or is there no way to build a file for Dad at Gedmatch?

                          I saw in their forums discussion of a phased missing parent's file, so someone appears to have done it (or maybe it's only one child). However, I googled an article by someone who says the phased children's files can't be added together.

                          Sorry for the basic questions, but this is the basic forum. :-)

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                          • #14
                            I feel pretty stupid here. The raw data files I have from FT-DNA are in the form "filename.csv.gz"

                            File won't open with notepad. Also doesn't seem to want to unzip.

                            Is this the correct raw data file to use to make the dummy file?

                            Kathy

                            Comment


                            • #15
                              Originally posted by GoofusBroadway View Post
                              I feel pretty stupid here. The raw data files I have from FT-DNA are in the form "filename.csv.gz"

                              File won't open with notepad. Also doesn't seem to want to unzip.

                              Is this the correct raw data file to use to make the dummy file?

                              Kathy
                              If still has the .qz at the end, you will need to unzip first. When unzipped it will be a .csv file which will open in notepad. I use WinRAR to unzip, but there are many other programs which are free if you do not have a program that will unzip

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