GEDmatch.com Adds Phasing Tool

Today (or perhaps yesterday?) popular DIY genomics website GEDmatch.com released a new tool for phasing DNA data.  Listed under a link entitled “Generate phased data file,” the tool allows users of the GEDmatch.com site to phase their chromosomes if they have their parent’s raw data.

(A similar tool was previously created by David Pike at http://www.math.mun.ca/~dapike/FF23utils/; with David’s tool, users receive their results directly and do not need to upload their DNA test results; accordingly, users have a variety of options depending on their privacy tolerance).

What the Heck is “Phasing”?

Currently, SNP chip testing performed by 23andMe or Family Tree DNA is unable to attribute a test result to either one of your parents.  For example, if your results for SNP rs00000 are “AG,” the test alone cannot determine whether the “A” came from your mother or father.

“Phasing” refers to the process of separating the mixed DNA results (the “AG”) into the DNA obtained from your mother (the “A”) and the DNA obtained from your father (the “G”).  This is typically done by comparing your results to your parents’ results and determining which parent could have and/or must have contributed each SNP.

For example, if mother’s results are “AA” at rs00000, and father’s results are “GA” at rs0000, then the data can be phased into “A” from mom and “G” from dad (since only dad could have contributed the “G”).  Every once in a while, the data can’t be phased, however (say you’re “AG,” mom is “AG,” and dad is “AG”).

What Good is Phasing?

Many genealogists are using phased data to identify which DNA came from individual grandparents, great-grandparents, and beyond.  I won’t get into that in detail now, but hope to at some point in the future (and eventually in the book I’m working on!).

As another example of using phased data, I used the new GEDmatch.com tool to phase my data.  Both my parents and I had previously uploaded our 23andMe and FTDNA data into GEDmatch.  I then performed some admixture analysis to compare unphased v. phased data.

Here is my unphased chromosome painting (Dodecad World9):

For comparison, here is my chromosome painting using the DNA I obtained from my father (same settings):

And here is my chromosome painting using the DNA I obtained from my mother (same settings):

Note that since this is so early I can’t say for certain whether using phased data creates some unwanted effects on the analysis (I’d love some input on that).  It is interesting, however, to compare the results of phased v. unphased data.

What uses will you put your phased data to?

6 Responses

  1. Patricia Baron 10 July 2012 / 11:15 am

    I was in hopes I could use the phased report to clarify mom from dad since I am adopted. My birth mom took the dna test for me after I did mine. Not sure how accurate the reports I got would be. I keep holding out hope of someday being able to discern what matches could be from my unk fathers side.

    • Penny Betz 7 April 2016 / 10:32 am

      Hi Patrica,

      Using Gedmatch, do a one-to-many comparison for yourself. Then do a one to many comparison for your phased data from your birth mother (The P ——— M1 number you get once you use the phasing feature.) Everyone on your first list for yourself who does not match your birth mother (is not on her list) should be paternal matches.

      I am adopted and was able to get my half-sibling names from my adoption agency in California (they recently changed the law so they will search for known siblings for you). My maternal half-sisters are very welcoming and they did FTDNA tests which I uploaded to Gedmatch. I used their results to find a paternal 2nd cousin who led to the name of my birth father and I learned about his life and could build a large paternal family tree. Many adoptees are able to find 2nd or even 1st cousins by doing DNA tests at all 3 companies to widen your chance of finding a close cousin match. My only other 2nd cousin match I have so far is at Ancestry.com and she has an unknown father! By building out my family tree we think we located her birth father, so it is possible.

      Good luck! It was so exciting to finally find my birth mother’s name in 2014 and find my birth father through DNA in 2015. I suggest reading blogs by dnajunkie, thegeneticgenaealogist, and kitty coopers blog to also learn about chromosome mapping. It is time consuming but is also a possible way to use your results from all 3 DNA testing companies to search for paternal matches. You are very lucky to have your birth mother’s DNA results!

      • AVANGELENE VON WHIPPLE 29 June 2016 / 2:59 pm

        i am new to the whole dna thing,i am trying to find unknown birth father and i took a dna test with 23andme.com.i do know most of my mothers side of the family (she has taken a dna test with ftdna but it is still processing),i share matches with surnames ive never reconized so i know its from my fathers side..how do i start to find my bio father with the autosomal dna with gedcom/gedmatch or wikitree?

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  3. Dan Brennan 29 January 2015 / 3:57 pm

    Call me dense but I’m trying to figure out what the use of the phasing tool is if I already have both parents, or if I only have my father what is the point in creating a phased account for him?

  4. PCaverly 5 June 2015 / 10:49 am

    If a man does not know who his biological father is, there are some other methods that can help in FamilyFinder. If the man has a sibling and they know for sure who the father is then testing this sibling should help sort out FamilyFinder matches. Both individuals have the same mother but different fathers. If in using FamilyFinder you sort matches so those that only match the sibling are likely from the maternal side (both testers have the same mother). Now we are left with other matches that only show on the man’s matches and therefore are likely connected to his paternal side. Of course we often find we get many matches so that is just the start of digging deeper. Very distant cousins, 5th or higher are difficult to find a common ancestor since they go back so many generations. If we find someone who is a 1st or 2nd cousin we have a better chance of narrow down a common ancestor. All of this means you still need to have a good genealogy database of ancestors to possibly find the link.

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