Getting Started with Genome Mate Pro, Part 10 — Import GEDmatch Triangulations

Scroll down for links to other posts in this series.

And now for the GEDmatch import we’ve all been waiting for:  Triangulations!

Segment triangulation is a technique grounded in the fact that we have two copies of each autosomal chromosome: one inherited from our mother and one from our father.  (Women also have two copies of the X chromosome, while men have only one.)

Because each autosomal chromosome has a so-called “homologous” copy (meaning “same general features or make-up”), two people could match me at the “same” spot in the genome yet not match one another, because one is related on my maternal side and one on my paternal. The graphic below illustrates what I mean:  my maternal chromosome is in red, my paternal in blue, and the two matches in grey, because I’m not sure yet on which side they are.

Triangulation involves comparing the two (or more) other matches directly to one another.  If they match each other, they are both related on the same side of my family (i.e., either through my mother or my father), like so:

And if they do not match one another, each is related to me through a different parent.

 

The data in the triangulation import allows us to tell the difference (even if you don’t have parents tested).  This import (and others like it) are what make GMP so powerful.

I recommend using the Chrome internet browser for GEDmatch imports.

Run the Tier 1 Triangulation Report at GEDmatch

1. Log into GEDmatch using your internet browser, and click on the link to the Tier 1 Triangulation tool.
   
2. Enter the GEDmatch kit number, set the Upper Segment Threshold Limit to “No Limit”, and select the radio button beside “Show results sorted by chromosome, segment start position”.
   
3. Click the TRIANGULATE button. This will take a while.  As the search progresses, you will see a growing string of asterisks.  Do not close this browser window or let your computer go to sleep while the triangulation search is running.  You should be able to work in other windows while the search is running.
   
4. When the report is done, you will see a big table of results. Select and copy everything on the page (control-a then control-c on a PC; command-a then command-c on a Mac).
   

 

Import GEDmatch Triangulation Results into GMP

1. Open GMP and back up your database (File > Backup Database).
2. Go to the Chromosomes tab. Using the Import Data menu, select “From GedMatch Tier 1”, then “2: Triangulation”.
   
3. Click OK to dismiss the pop-up with instructions.
4. In the next window, click the PASTE button then the IMPORT button.
   
5. When the import is done, glance at the pop-up summary to see how many triangulations were added, then click the CLOSE button.
   
6. Look at the Chromosomes tab again. Does anything look different? Nope. But something really important has happened!

 

Working with Triangulations

1. In the Chromosomes tab, pick a close-ish relative and right-click on their name. I’ll use Cousin Bryan (because I always use Cousin Bryan!)
   
2. Wait!  What’s this? Holy smokes! There’s an entire slew of options there!  Turns out a lot of the “good stuff” in GMP is lurking beneath the right-click button of your mouse. This makes powerful tools available with a single click without cluttering up the interface. You will find these right-click features available throughout GMP. (Go ahead, try it!)
3. Select “Show Overlapping DNA Segments”. This will filter your view to only show matches with segments that overlap the one you selected.
   
4. Overlapping doesn’t necessarily mean triangulating, as described in the opening paragraphs of this post. Unless the two (or more) matches also match one another, we can’t be sure that they’re related to us on the same side.
5. Right-click on your close-ish relative again, but this time select “Show Possible Triangulations”.
   The number of matches shown has probably gotten smaller. In fact, toggle back and forth between “Show Overlapping DNA Segments” and “Show Possible Triangulations” to compare.
6. Hit the Escape (esc) button to remove the filtering and see all of your matches on that chromosome again.
7. If you’ve tested one or both of your parents, you can quickly assign all of your matches on this chromosome to a side using the right-click options.  First, make sure the segment shared with your parent has the appropriate designation (M or P) in the “Side” field.
8. Right-click on that parent and select “Show Possible Triangulations” to filter the visible segments.
9. Right-click again on that parent and select “Mark shown DNA segments”.
   Now, all of those filtered segments should be marked to that side (M or P).
10. But wait! There’s more! Rather than filtering the visible segments and going chromosome by chromosome, you can right-click on a parent and instead select “Mark All Unknown DNA Segments Triangulated With”.
    Now, switch to a different chromosome.  You should see that GMP has assigned  sides to segments on all of your chromosomes based on triangulation to that parent. (NOTE: GMP sometimes skips segments it should be able to assign … I’m not sure why.)
11. If you’ve tested both parents, do the same thing with the other one: make sure the “Side” is designated for that parent, then right-click and select “Mark All Unknown DNA Segments Triangulated With”.
12. Once you’ve done your parent(s), you can similarly assign segments using more distant relatives. For example, with just a few clicks, I can find segments that triangulate with Cousin Bryan (“Show Possible Triangulations”) and assign them to a group name (“Mark Shown DNA Segments”). For example, I could use the MRCA names “Sid and Julia”; the village they were from, “Patoutville”; or whatever strikes my fancy. The exception will be matching segments that have already been assigned to an MRCA in the RELATIVE DETAIL tab. In the screenshot below, Mary was not assigned to “Patoutville” because her segment had previously been assigned to an MRCA (indicated by the fact that her name is in bold).
    
13. Continue to explore “Side” and “Group” assignments on your own.

 

Getting Started with Genome Mate Pro Series

• Part 1 — Install the Program
• Part 2 — Set Up a Profile for a GEDmatch User
• Part 3 — Activate GEDmatch Import Templates
• Part 4 — App Settings
• Part 5 — First GEDmatch Imports
• Part 6 — The Chromosome Browser
• Part 7 — More GEDmatch Imports
• Part 8 — The Relative Detail Tab
• Part 9 — Import a Gedcom
• Part 10 — Import GEDmatch Triangulations
• Part 11 — Install the DNAGedcom Client
• Part 12 — Use the DNAGedcom Client to Import FTDNA Data
• Part 13 — Merge Duplicates (coming soon!)
• Part 14 — The Relative List Tab (coming soon!)
• Part 15 — A Few Tips (coming soon!)
• Part 16 — Use the DNAGedcom Client to Import 23andMe Data (coming soon!)
• Part 17 — Import Ancestry Composition from 23andMe (coming soon!)
• Part 18 —Use the DNAGedcom Client to Import AncestryDNA Data (coming soon!)
• Part 19 — The Segment Map Tab (coming soon!)
• Part 20 — Create Custom Templates for MyHeritage (and Others) (coming soon!)
• Part 21 — Customize Genome Mate Pro (coming soon!)
• Part 22 — Update Your GMP Version