Using GEDmatch (The Triangulation Tool)

The previous article in this series is Using Genome Mate (Add confirmed segments to chromosome map).

As explained in my earlier post, Using Genome Mate (Identify triangulated groups and confirm segments), we now have an understanding of the basic principals of triangulating DNA segments, and know how to manually go through our match data and identify triangulated groups. In this post, I will show how to use the GEDmatch Triangulation tool to automatically identify the triangulated segments you share with your 400 closest matches at GEDmatch and then easily import the triangulated segment results from GEDmatch into Genome Mate.

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.

In order to use the Gedmatch Triangulation tool, you need to be a subscriber to the GEDmatch Tier 1 service. The cost for the Tier 1 service is $10 per month, and you can subscribe in increments as little as a month at a time. Tier 1 service is well worth the nominal cost, even if you use it for nothing more than the Triangulation tool. In addition to the Triangulation tool, however, Tier 1 service will also provide you access to the Matching Segment Search tool, the Relationship Tree projection tool, and the Lazurus tool, and the use of these three tools will be covered in future posts. The instructions for subscribing to the Tier 1 service are located at the bottom of the GEDmatch main page (http://www.gedmatch.com), after you’ve signed in.

After subscribing to the Tier 1 service, and signing back in to the GEDmatch website, you will see an additional blue box at the lower right of the GEDmatch main page showing the Tier 1 Utilities.

1) In the Tier 1 Utilities box, click on the Triangulation tool link.

2) Clicking on the Triangulation tool link will bring up the GEDmatch Segment Triangulation page. Enter your kit number in the first box, select No Limit in the Upper Segment Threshold Limit dropdown, click the “Show results sorted by chromosome, segment start position” radio button, and then click the Triangulate button at the bottom.

3) After clicking the Triangulate button, you will get a new page which says “Progress is shown by a string of 400 asterisks (‘*’) on the lines below:” on the last line.

Asterisks will begin slowly appearing in black, with every tenth asterisk appearing in red. This is the indication that the Triangulation tool is processing your results. The processing can take up to forty-five minutes to completely finish. It is very important to let this processing finish, and not interrupt it by clicking the stop or refresh buttons on your browser, closing your browser, or navigating to another page in your browser. If you do happen to interrupt this processing, open a new browser window/tab or restart your Internet browser, log back in to the GEDmatch page (http://www.gedmatch.com), and repeat steps 1 through 3 above.

Once the Triangulation tool has completely finished processing, you will receive a results page that resembles the following screenshot.

4) While viewing your results screen, select everything on the page (Windows users hold down the Control key and press the A key on your keyboard, Mac users hold down the Command ⌘ key and press the A key on your keyboard). Copy the data (Windows users hold down the Control key and press the C key on your keyboard, Mac users hold down the Command ⌘ key and press the C key on your keyboard), and then switch to your Genome Mate software.

5) In Genome Mate, after making sure you have first backed up your database, click on the Import Data link in the menu bar near the top of the main Genome Mate window.

6) 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 (4) Copy/Paste GedMatch Tier 1 Triangulation ICW link in the GedMatch Import Options section.

7) Clicking on the (4) Copy/Paste GedMatch Tier 1 Triangulation ICW link in the GedMatch Import Options section will bring up another Import Data window.

8) Click once inside the rectangular box, and then paste the data you previously copied from GEDmatch (Windows users hold down the Control key and press the V key on your keyboard, Mac users hold down the Command key and press the V key on your keyboard). After pasting your data into the box, click on the Format button. [Note: Although the instructions warn that only the Chrome and Firefox browsers are supported, I have found that as of Genome Mate version 1.2.19, the Safari browser also works in most cases.]

9) Clicking on the Format button will bring up the Import Summary window. This acts as a confirmation that the data was imported, as long as ICW records processed is not 0 (zero). If ICW records processed is zero, this is letting you know that you have previously imported all these ICW records, or is an indication that something went wrong with your import.

If you have not imported these ICW records before, and something seems to have went wrong with your import, you should click the Close button and repeat steps 4 through 8 above. If you have repeated steps 4 through 8 above, and are still getting a zero for ICW records processed, please let me know by adding a comment to this blog post, or by sending me an email, so that I can help you determine what is causing the problem you are experiencing.

After having imported your ICW records, click the Close button.

After clicking the Close button, you will be taken back to the main Genome Mate window. It is a good idea to get in the habit of backing up your Genome Mate database after each import you do. In front of most, if not all, of your matching kits from GEDmatch, you will notice a small symbol that looks like four people standing together. This is the indication that ICW (in common with) data exists for that match.

Moving your mouse pointer over one of these symbols will highlight all the other matches of yours who also match the person whose symbol your mouse pointer is currently over.

Clicking on the symbol will then bring up a box that allows you to set the ICW Group for all of these highlighted segments (for an explanation of the principles of setting ICW Groups, please see my post Using Genome Mate (Add confirmed segments to chromosome map).

If you know whether the highlighted group matches on the paternal or maternal side of your family tree, it is best to correspondingly mark the highlighted segments as either P or M. If you don’t yet know whether the highlighted group matches on the paternal or maternal side of your family tree, however, you can still make use of this feature.

Instead of marking the ICW Group as either P or M, instead mark all the highlighted segments with a designation you’ve decided upon that represents the group has been triangulated but is still undetermined as to which side of your tree the group matches you on. For example, I use the letters A and B. You could also use the numbers 1 and 2. Anything will work for this purpose, other than using the letters P and M, or an asterisk (*).

Here, I have marked all the highlighted segments as A.

Any segments that line up vertically with the segments I’ve just marked as ICW Group A, but aren’t part of ICW Group A, I mark with ICW Group B, since I know it is extremely likely they will match on the opposite side of my family tree from the side ICW Group A matches me on.

This lets me know, as I look through my chromosomes in Genome Mate, that I’ve identified the triangulation group, but still need to work on finding out which side of my family tree the group matches me on.

Once I am able to determine the correct side (paternal or maternal) a group matches me on, however, I can mark all of the segments in that group as either ICW Group P or ICW Group M, whichever the case may be. I then mark the other group I previously designated as the ICW Group of the opposite side of my family tree.

For example, let’s say that I discover a first cousin on my mom’s side of my family tree shares the same segment of chromosome 1 with me as with one of my matches from ICW Group B. I can then mark ICW Group B as M, and mark ICW Group A as P.

If you are fortunate enough to have been able to test a parent and/or grandparent, the Triangulation tool simplifies things even further. In the example shown below, I use the symbol in front of my mother’s test on the first line to highlight and mark the ICW Group as M of all the matches shared between me and my mother.

In the next example shown below, I use the symbol in front of my paternal grandmother’s test on the third line to highlight and mark the ICW Group as PGM of all the matches I share with my grandmother. [Note: After marking all of the segments shared with my paternal grandmother as PGM, I go back and set the ICW Group of my father’s test on the second line to correctly be just P, rather than PGM, since the matches I share with my father come from both sides of his ancestral family tree.]

I hope this information is helpful. Using the GEDmatch Triangulation tool, in conjunction with Genome Mate, should greatly speed up your identification of triangulated groups of segments, allowing you to more efficiently begin working with the matches in these groups to try to identify the common shared ancestor(s) for each group.

As with all my posts, if you experience any problems while following these steps, notice that a screen has changed dramatically from what I’ve shown in the screenshots, or have an easier/better way to accomplish what I’ve shown, please let me know by commenting on this thread or sending me an email. Thank you.

This article last updated 10 Jan 2015