Introduction To Using GEDmatch

This is the first post in my series on how to use GEDmatch (http://www.gedmatch.com). My goal in writing this post is to provide an introduction to using GEDmatch to do comparisons, and explain the basic fundamentals of chromosome mapping, in an easy to understand manner with simple to follow instructions.

Being able to determine the identification of which specific portions of your DNA were contributed by which ancestors is called chromosome mapping. We do this by using a process called triangulation. In it’s most basic form, the principle of triangulation is that if three people match each other in the same part of their DNA, and also share the same ancestor(s), that part of their DNA is most likely to have come from the most recent ancestor(s) the three people all share in common.

Here is an example. This is a screen shot showing a comparison between my mother, a first cousin one time removed, and a second cousin. On the left hand side of the graph, you will see there is a section where all three line up in the same spot. This is also shown in the middle box of the third row of the table. The three of them share the same segment of chromosome 3, ranging from a start position of 13161109 to an end position of 21761222, with a segment length of 11.0711 cM (centimorgans). The centimorgan rating is an indication of the quality of the match, and I will explain more about this in an upcoming post.

Looking at the direct line ancestors of my mother and her two cousins, the first ancestors all three of them share as direct line ancestors are one of my mother’s sets of great grandparents, John Isaac Egbert and Eliza Jane Seaver. As my mother and her two cousins descend through different branches of this same couple, I can say it is extremely likely this segment of DNA on chromosome 3 was passed down from John and Eliza, since I also know my mother’s two cousins match each other on this same segment of chromosome 3 (known from previous comparisons I’ve done). When people share a match with another person, this is referred to as in common with (frequently abbreviated as ICW in discussions about genetic genealogy). After doing these comparisons, and locating the most recent common ancestor(s), this segment can be said to have been properly triangulated.

As I continue doing comparisons with other people, if I come across anyone who matches my mother in this same segment of chromosome 3, and also matches my mother’s two cousins, I know it is extremely likely this other person is a descendant of John and Eliza, or is a descendant of one or more direct line ancestors of John and/or Eliza.

While the comparison data can be recorded and maintained in a spreadsheet, I think you will find this is where the Genome Mate software really makes things much easier, as well as making potential matches much easier to spot. Here is how the comparison between my mother and her two cousins looks in Genome Mate.

You can see my mother’s two cousins (in the shades of green) lining up, just as we saw in the GEDmatch screenshot. In addition to overlapping myself, you can see my mother’s two cousins also overlap two other people. My mother’s two cousins share ancestry on the paternal side of my mother’s ancestral family. R E H is my mother’s uncle on the maternal side of her family. He is not a match to either of my mother’s two cousins. The very bottom person shown, however, overlaps both of my mother’s two cousins, and also in turn matches each of them (known from previous comparisons I’ve done). I have contacted this person to ask if they are a descendant of John Isaac Egbert and Eliza Jane Seaver, or is a descendant of one or more of the direct line ancestors of John and/or Eliza.

This is how your ancestral lines can be verified, as well as used to locate additional relatives who may then provide you with clues to be able to extend your ancestral line further back. While the likelihood of this additional person sharing Egbert and/or Seaver ancestry is extremely likely, they may not yet have their family tree back far enough to be able to verify who our most recent common ancestor(s) is/are (frequently abbreviated as MRCA in discussions about genetic genealogy).

As shown in this example, it’s important to keep in mind that someone else could match you on just the paternal side of your ancestral family, on just the maternal side of your ancestral family, or on both sides of your ancestral family. This is why triangulation is needed in order to properly determine from which line(s) you and your match share common ancestry. Now, let’s go about learning how to do DNA comparisons between two people, and how to record this data.

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.

Step 1) To get started, log in to your GEDmatch profile. If you do not yet have a GEDmatch profile set up, please take a look at steps one through four of my previous post How To Upload Your Ancestry DNA Test Results To GEDmatch for a guide to setting up a GEDmatch account and profile.

Upon logging in, you will be taken to the GEDmatch home page, which will look similar to the following screen shot. Your home page may appear slightly different, as GEDmatch has recently had some features turned off while doing some upgrades, and is now gradually starting to make these features available again. Click on the ‘One-to-one’ compare link in the white DNA Raw Data box inside the darker blue Analyze Your Data box in the lower right of the page.

Step 2) You will be taken to the GEDmatch.Com DNA one-to-one Comparison Entry Form page.

[A note for those of you using Genome Mate to follow along with this example exercise] Please make sure you have backed up your database prior to beginning, are using the test profile you created (as shown about halfway through my post on setting up Genome Mate) and not your real profile, and that you edit your test profile to add the GEDmatch kit # of A890051 in the Manage Kit Profiles box (found by clicking Profiles in the menu bar near the top of the program window).

In this example exercise, we will be using the kit numbers of myself (A890051), my mother (A776948), and my mother’s uncle (A242029). The same steps and methods I will be showing can later be used with your own GEDmatch data and your real Genome Mate profile.

On the ‘One-to-one’ comparison page, enter A890051 for Kit Number 1 and A776948 for Kit Number 2. Leave the rest of the settings and boxes as they are, and click the Submit button at the bottom.

Step 3) Clicking the Submit button will bring up the GEDmatch.Com Autosomal Comparison screen. Select everything on the page (Windows users hold down the Control key and the A key on your keyboard, Mac users hold down the Command key and the A key on your keyboard). Copy the data (Windows users hold down the Control key and the C key on your keyboard, Mac users hold down the Command key and the C key on your keyboard), and then go to your Genome Mate software.

Step 4) In Genome Mate, after checking to make sure you have backed up your database and are using your test profile, click on the Import Data link in the menu bar near the top of the program window.

Step 5) Clicking on the Import Data link will bring up the Import Data window. Select the radio button next to GedMatch in the Select Data Source section, and then click on the Copy/Paste GedMatch 1 to 1 Comparison Matches link in the GedMatch Import Options section.

Step 6) Clicking on the Copy/Paste GedMatch 1 to 1 Comparison Matches link in the GedMatch Import Options section will bring up another Import Data window. Click inside the rectangular box, and then paste the data you previously copied from GEDmatch (Windows users hold down the Control key and the V key on your keyboard, Mac users hold down the Command key and the V key on your keyboard). Although the instructions warn that only the Chrome and Firefox browsers are supported, I have found that as of version 1.2.19 of Genome Mate, the Safari browser also works. After pasting your data into the box, click on the Format button.

Step 7) Clicking the Format button will bring up yet another Import Data window, showing the chromosomes and segments that are about to be imported. Before continuing, it’s always a good idea to make sure the profile listed is the one you want to import data to. After making sure you are importing to the correct profile, Click on the Add Data button.

Step 8) Clicking on the Add Data button will bring up the Import Summary window. This acts as a confirmation that the data was imported, as long as Matches Added and Relative records added are not both 0 (zero). If they are both zero, this is letting you know that something went wrong, and you should repeat steps 3 through 7 above. While it may initially cause concern, there will always be something listed in the Rejected for invalid format category. This is a byproduct of the data conversion process, and is not an indication of a problem unless Matches Added and Relative records added are both 0 (zero). After verifying you do not have zeros for both Matches Added and Relative records added, click the Close button.

Step 9) Clicking the Close button returns you to the previous Import Data window, minus the Add Data button, and you can now click the Close button in the Import Data window.

Step 10) Clicking the Close button in the Import Data window will return you to the main Genome Mate screen, with the first of our imported matches now showing. Newly imported matches are highlighted in blue for a few days to help differentiate them from existing matches as you continue accumulating more and more match data.

Step 11) Now that we’ve successfully imported our first match, repeat these steps, but this time import the match data for my mother’s uncle (kit number A242029 in place of kit number A776948). When finished, you should have a screen which looks like the following:

Congratulations, we have completed doing two comparisons, and have imported this data into Genome Mate. We are now ready to begin working with that data, and the next post in this series will begin showing how to use the tools that are available on the GEDmatch site and in the Genome Mate software. Before closing the Genome Mate software, remember to backup your database file.

If you experience any problems while following these steps, 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. Thanks for reading.

The next article in this series is Introduction To Using GEDmatch Part 2 (The One-To-Many Comparison Tool).

This article last updated 18 Oct 2014