Using GEDmatch Part 6 (The Phasing Tool)

The previous article in this series is Using GEDmatch Part 5 (Alternate To Triangulation Tool).

Twice within the past week, I’ve come across situations where the GEDmatch phasing tool would be very likely to help solve someone’s genealogical mystery. It seems some people may not be aware of this extremely useful, yet easy to use, tool. Therefore, I thought it would be a good idea to write a few words explaining a bit about what the phasing tool does, and what the benefits of using it are, as well as show the very quick and simple steps to using the tool.

The basics of the phasing tool are that it will take the test results of a child and one, or both, of their parents, and create two GEDmatch test kits. One of these test kits will be just the mother’s DNA, and the other will be just the father’s DNA. Using these two test kits for doing comparisons has a couple of advantages.

The most obvious of these advantages is that in cases where you are only able to test a child and one parent, the test of the other parent can be extrapolated and simulated. This simulated (phased) kit then acts as a substitute in running the available tools on GEDmatch, including one to one and one to many comparisons. While the phased test kits that are created are the most accurate when the tests of a child and both parents are available, the accuracy is reduced only slightly when just the test of a child and one parent are available. In cases of adoption, or non-paternity events, the phased kit can then used to search for matches to help with identifying the unknown parent.

Some words of caution: Please exercise appropriate care and discretion in either of these situations. The revelation of information related to either of these events can potentially have devastating effects. There are people who may prefer not to know about such a situation having taken place, or do not want it to be brought up. Be sure to respect the wishes and privacy of others at all times during your searches.

In cases where the child and both parents have tested, generating phased kits has the advantage of noticeably increasing the confidence level that a shared segment with someone is indeed a valid match, and not just a match by random chance or a false positive, when using the GEDmatch tools with your phased kits.

Click here if you’d like to open the GEDmatch website in a new window/tab to make it easier to follow along with these steps.

Prior to using the phasing tool, a GEDmatch profile needs to be setup, and have the test results of a child, and one or both parents, already uploaded. If you have not done this yet, and need help with doing so, please see my previous blog post Introduction To Using GEDmatch.

1) To use the phasing tool, log in to GEDmatch and click on the ‘Phasing link in the white DNA Raw Data box inside the darker blue Analyze Your Data box in the lower right of the page.

Using GEDmatch - Phasing Step 1

2) Clicking on the Phasing link will take you to the GEDmatch.Com Phased data generator Data entry form page. The entry form is pretty straightforward. You need to enter the GEDmatch kit number of the child’s test in the first box, and the GEDmatch kit number of either the mother’s test, or the father’s test, or both, in the corresponding box/boxes. Once you have finished entering the kit numbers, click on the Submit button.

Using GEDmatch - Phasing Step 2

3) That’s all there is to generating the request to create the two phased test kits. You will see a notice about allowing for processing time for the kits to be created. While this process used to take up to eight weeks to complete, the process is now completing in about two days time. When you return to your GEDmatch home page, you will see that the request has been generated, as indicated by the two test kits that have red asterisks in front of them, and begin with the letter P (for phased) in the kit number. One kit will end with M1, and the other with P1. These are indicating the maternal kit and paternal kit, respectively. Between the P and the M1/P1 will be the kit number of the child.

Using GEDmatch - Phasing Step 3

Once the required processing time has completed, the two phased kits will be ready to be used, as indicated by the lack of asterisks before the kit number.

Using GEDmatch - Phasing Step 4

These two phased kits can now be used just as if the child’s biological mother and father had tested and had their test results uploaded to GEDmatch. These two kits will be automatically flagged as research kits only. Research kits can be used with any GEDmatch utility, but they will not be shown in comparison results for other kits. If someone else runs a one to many comparison against their test, for example, these phased kits will not be among the results shown to them. Phased kits are not allowed to be public on GEDmatch, in keeping with the concerns I raised in my words of caution above.

I hope this may help some people break through some of their genealogical brick walls. I’m sure there are other uses for these phased kits that I haven’t yet fully explored (such as the ethnicity and admixture tools), or uses that I haven’t yet discovered. If you come across any, I hope you will please share them here.

If you experience any problems while following these steps, discover any errors I’ve made, or notice that a screen has changed from what I’ve shown in the screenshots, please let me know by commenting on this thread or sending me an email. Thank you.

This article last updated 31 Oct 2014

Advertisements

13 thoughts on “Using GEDmatch Part 6 (The Phasing Tool)

  1. Pingback: Using GEDmatch Part 5 (Alternate To Triangulation Tool) | Adventures In Genealogy Research: No Stone Unturned/The Wright Stuff

  2. I have my results and my mother’s but my father has passed away. I do have his brother’s data though. Would there be any benefit to using my uncle’s in place of my father’s or would it be better to just use my mother’s with this phasing tool?

    • Since you have both your results and your mother’s results, I would recommend using the phasing tool to generate a phased kit for your father. The matches to your father’s phased kit can then be further verified by comparisons with your uncle’s results.

  3. I am adopted and I know my maternal side of the family…my mother, however, is not playing ball (what a spoiled sport), but my maternal aunt has tested and uploaded to GEDmatch. I went ahead and used her as my mother (I know, but it was as good as I could get it) so that I could try and determine my paternity. I also have a potential paternal first cousin who SAID that he tested, but I question his honesty (I think he may have had his wife do the test instead). Currently, I am trying to prove that one. Maybe the phasing can help me figure this all out. 🙂

    • Hi Pam,

      That’s very unfortunate about your mom not being agreeable to testing. Perhaps, one day she may have a change of heart. If you haven’t already done so, you may want to reassure her regarding the privacy of any genealogical DNA testing, and that initials (or even a pseudonym) can be used rather than a full name. I’ve had some potential testers, who initially said no to testing, change their mind and agree to test, when they found out this was the case.

      Given the circumstances you’ve outlined, using your maternal aunt as a substitute for your mother in the phasing tool is certainly worth a try. As it sounds like you are already aware, just be really careful not to jump to any quick conclusions with potential matches to the phased paternal kit, and proceed slowly and cautiously as you work through the match list.

      In regards to the potential paternal first cousin, this is a close enough relation that there should be a significant amount of matching DNA with you if he truly is your first cousin. You can run a one to one comparison, and then compare the total amount of shared DNA with the chart at ISOGG (http://www.isogg.org/wiki/Autosomal_DNA_statistics). In the case of a first cousin, the amount should be around roughly 850 cM, although this can be highly variable. If the total amount you share with him is around this amount, then use the People who match both kits, or 1 of 2 kits tool at GEDmatch to check for common matches you share with this first cousin.

      Thanks for your comments, and I hope this is of some help. I wish you all the best for success with your search for your father.

      Dan

  4. Is there any point in doing a one-to-one comparison of the child after phasing back to the phased results of the missing parent? shouldn’t it look similar to a one to one with the tested parent to child?

    • Hi Bonnie,

      I’m not sure I’m properly understanding your questions, so if my answer seems wrong or seems to fail to address what you were asking, please let me know.

      In regards to whether there is any point in doing a one to one comparison of the child to the matches with the phased kit of the missing parent, I think it is just personal preference as to if this is of any value. If create a separate profile for the phased kit of the missing parent, then I think it is useful to do a one to one comparison of the child to the matches with the phased kit of the missing parent so that you will have this information in the profile of the child. If you don’t create a separate profile for the phased kit of the missing parent, then there is probably not much benefit in it.

      In either case, I would encourage you to use the Tier 1 Triangulation tool after the phased parent kits have been generated, as shown in . This will take care of doing the one to one comparisons with all of the closest matches (up to 400).

  5. This is an amazing tool that gedmatch has to offer!!! My mind is swimming with the possibilities on what I could do with it (I have an ornery father who doesn’t want to take the test, though he’s already done the ydna test some years ago). He has early stage alzheimers so I’m not sure if that has an impact on his answer or not. Anyway, my mother and I have taken the test. And several of my cousins (from my father’s branch) have taken the test. And a few of my 1/2 siblings from my dad are willing to take the test. We have come together as a family (those of us interested in breaking down the brick walls… many due to slavery…. and have discussed the ramifications of doing the dna tests, have prepared ourselves for any surprises, etc. and have a plan of action if we do come up with something that may be sensitive or surprising.

    With that said, I’m wondering if you could answer some questions for me:

    1. I assume that the phasing tool would only extrapolate approximately 1/2 of the dna of the parent who didn’t take the test. since we each only inherit about that much from each parent.(still better than nothing). But for people who have living full-siblings, each sibling can test and each research kit can be used (together) to extrapolate an even more of a full profile the missing parent. For instance, I have a cousin whose father is deceased, but he has tested and so has his mother. He also has a full sibling as well (who hasn’t yet tested). To make things even for the purpose of guessing, we could say that each brother inherited exactly 50% from dad. BUT they both didn’t inherit the same 50%. say both brothers inherited 25% which was the same. but each inherited an additional 25% that was different (this is all from dad). so the brothers overlap on 25% of the dad’s dna. but each also inherited a different 25% of his dna

    So if both brothers test, and both build separate phased research kits. Comparing/combining both research kits should provide a 75% percent complete dna profile kit for dad? (of course that is based on the clean cut number of 25% which wouldn’t actually happen.

    So my first question is: Would the phasing tool only extrapolate approximately 1/2 of the dna of the parent who didn’t take the test?

    And the second question is: Based on the 25% examples I used above, if both brothers tested, and both build separate phased research kits. Would comparing/combining both research kits provide a 75% percent complete dna profile kit for dad?

    • Hi Samantha,

      It’s sounds like you and your family have very carefully considered all the possible benefits and ramifications of using DNA testing to help with your genealogy research, so I hope it is of great help to you in extending your family tree. While it’s unfortunate that your father is not interested in taking an autosomal DNA test, the tools at GEDmatch, in addition to all of your other family members who are willing to test, should help you overcome this.

      In regards to your questions about the percentage of your father’s DNA that can be extrapolated, your breakdown of the inheritance numbers looks to be correct, but the percentages are just hypothetical averages (as I’m certain you are aware), so I wouldn’t get too worried about specific numbers/percentages. As you said, anything is better than nothing, and the more people that test the more comparisons can be done and the better the results.

      In addition to using the phasing tool, you should take a look at the GEDmatch Tier 1 Lazarus tool (which I have not covered yet in a blog post). With all the available testers you have listed, the Lazarus tool should produce a kit for your father that will serve as a nice complement to the kit for your father generated by the phasing tool. There is a nice two part writeup of the Lazarus tool on Blaine Bettinger’s blog (http://www.thegeneticgenealogist.com/2014/12/09/recreating-grandmothers-genome-part-1/).

      Thanks for your comments and questions, and best of luck on your quest to break down your brick walls!

      Dan

      • Do you have any information, or instructions on using (Relationship Tree projection)in Tier 1 utilities at GEDmatch?

      • Hi James, sorry to be taking several days to see your question and reply. I don’t currently have any instructions for the Relationship Tree projection. I’ll take a look at it and see what I can come up with for a step by step guide. Thanks, Dan

  6. My DNA and my maternal grandmother and maternal grandfather’s DNA are on Gedmatch. Not my mom or my dad’s. Could I run a phasing test with my maternal grandmother and grandfather’s kits? I imagine that would show me easily if my matches match via which grandparent, and if neither, that means the matches match via my father, yes? Will the tool allow me to do it when it’s not my parents? I don’t want to break Gedmatch running this, ha ha! Thanks for any help.

    • Hi Joanna,

      Using the phasing tool on GEDmatch with your results and your grandparent’s results wouldn’t break GEDmatch, but I’m uncertain whether you’d get any meaningful results from doing so. Instead, my suggestion would be to use Genome Mate Pro, and create profiles for yourself and both of your grandparents. Do a full set of GEDmatch imports for each of these three profiles. Then, for any of the matches in your profile, you can see if they match either of your grandparents, and if so, mark them accordingly. For any of your matches who don’t also match your maternal grandparents, you can generally mark them as being paternal matches, if you wish, but keep in mind that this is not an absolute. Your profile will have some matches that don’t actually match either of your parents, which you will be unable to identify for certain without having tests of your parents to compare against. If you elect to mark the segments that don’t match your maternal grandparents as paternal, my suggestion would be to mark them as P? (or something similar) so that going forward you are reminded this is not for certain. Hope this may be of some help, but it sounds like you already have a pretty good understanding of things and are well on your way.

      Best wishes on your research,

      Dan

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s