Getting Started with Genome Mate Pro, Part 5 — First GEDmatch Imports

In this lesson, we’re *finally* going to import some data from GEDmatch!

If you set up more than one profile, chose one (probably yourself), and do all of these steps with just that one profile to avoid accidentally mixing things up. Then, if you want to import data for another profile, repeat the steps for that other person.

During this exercise, we will be switching back and forth between GMP and your internet browser. You will want to have both programs open at the same time.

I recommend using the Chrome internet browser for GEDmatch imports.

 

Backup Your GMP Database and Check Your Settings

  1. Open GMP. In the menu bar at the top of the program (PC) or at the top of your computer (Mac), select “File” then “Backup Database”.
    You should back up before every import, so if something goes wrong you can easily restore your work.
  2. Go to the PROFILES tab.
  3. Click on your profile name in the Profile List in the left-hand panel and make sure that your GEDmatch number has been correctly entered in the “Match Keys” panel at the bottom center. (I can’t tell you how many times I’ve had an import fail because I neglected to do this quick check.  If your GEDmatch number is missing or incorrect, see Part 2 of the series.)

Run a “One-to-Many” Search at GEDmatch

  1. Switch to your internet browser and log into GEDmatch.
  2. From the main page, click the link for “One-to-many matches” in the panel titled “Analyze Your Data”.
  3. On the next page, enter your kit number and click the DISPLAY RESULTS button.  You do not need to change any other settings.The search will take only a few seconds.
  4. When the results have loaded, copy everything on the web page. To do this on a PC, type control-a (to select everything) then control-c (to copy it to memory). On a Mac, type command-a then command-c.

 

Import One-to-Many Data into GMP

  1. Switch back to GMP.
  2. Select your profile name in the pulldown to the left of the PROFILES tab (beneath the Genome Mate logo). You only need to do this if you set up more than one profile. If you only have one profile, yours will already be selected.
  3. Go to the CHROMOSOMES tab. Assuming you haven’t skipped ahead in the tutorial, you should see a whole lotta nuthin’: white space with horizontal lines.
  4. Using the Import Data menu, select “From GedMatch” then “1: Create Relatives Records via One to Many Matches”.
  5. The pop-up gives instructions for how to collect the data from GEDmatch, which we did in the previous section of this post. (Each import option has a similar guide, which is a really nice touch.) Click OK to dismiss it.
  6. The next pop-up asks you to confirm that the GEDmatch one-to-many results you are about to import are for the profile you currently have selected. If this is not the case, select the correct profile in the pulldown beneath the GMP logo.
  7. In the next window, click the PASTE button at the bottom to enter the one-to-many report, then click the IMPORT button. 
  8. The progress of the import is tracked at the very bottom of the GMP window. Don’t worry about skipped lines. Recall that GMP expects data to be in a table format, but the first few rows of the One-to-Many report are descriptive text rather than match data.  Those are the lines that GMP is skipping.The import should take about 5 minutes.
  9. When the import is done, you’ll see a pop-up that summarizes what happened. In my case, information for 1,998 matching relatives was added to GMP.
  10. You should still see a whole lotta nuthin’ in the CHROMOSOMES tab.  That’s because the one-to-many report from GEDmatch contains information like names, email addresses, and haplogroups, but not segment information. Try going to the RELATIVE LIST tab and choosing GedMatch from the “Select Source” pulldown at the top left.
  11. The window should fill with a list of matches in purple font with a yellow background. Purple is the default font for GEDmatch, and the yellow highlighting means those matches were recently imported.
  12. Play around with this window. Each of the columns is sortable. You can enter a “Side” (M for maternal, P for paternal), specify the relationship if you know it, and make notes about the MRCA.

Yeah, okay, I know:  that wasn’t particularly satisfying.  What you really want to do is import segment data, right?  If you’re game, so am I.  Let’s do it!

 

Run the Matching Segment Search at GEDmatch

  1. In your internet browser, log into GEDmatch. Under the Tier 1 Utilities toward the bottom of the main page, click on “Matching Segment Search”.
  2. On the next page, enter your kit number, select “No” for the option to “Show graphic bar for Chromosome?”, and click the SUBMIT button.
    The search should take 5 to 10 minutes.
  3. When the results have loaded, copy everything on the web page. (control-a then control-c on a PC; command-a then command-c on a Mac)

 

Import Matching Segment Search Data into GMP

  1. Switch back to GMP and the CHROMOSOMES tab.
  2. In the menu bar, select “Import Data”, then “From GedMatch Tier 1”, then “1: Matching Segment Search”.
  3. Click OK to dismiss the pop-up with instructions on how to get the data for this import (described in the previous section of this blog post).
  4. You’ll get another pop-up asking if you want to load the data into the profile that is currently active. If that’s the same person as in the Matching Segment Search at GEDmatch, click YES. If not, click NO, change profiles, and go back to Step 3.
  5. When the Matching Segment Search is done, switch to the GEDmatch window in your internet browser, and copy everything on that page (control-a then control-c on a PC, command-a then command-c on a Mac). Do not close your internet browser window yet!
  6. Now, switch back to the GMP window and click the PASTE button at the bottom left of the pop-up.
  7. Click IMPORT.
  8. At the bottom of the GMP window, you will see text telling you how far along the import is. Recall GMP skips lines that do not contain data in a table format (all those strings of asterisks in the search results … skipped).  If you have fewer than 100 skipped lines, fret not.
  9. Don’t get too excited when the number of DNA Segments Processed gets close to the total. Segment imports have two phases. The ticker at the bottom of the window will tally DNA Segments Processed, then will go through Triangulations Processed. Wait for both to complete.
  10. When both phases of the import are done, you’ll get a new pop-up summarizing how many segments were added and some other details. Click CLOSE.
  11. And now, the moment you’ve been waiting for! The window in the CHROMOSOMES tab should now contain loads of glorious segments against a yellow background. As in the RELATIVE DETAIL tab, the yellow highlighting means that those segments are newly imported. It will disappear after 2 days. (You can change the timeframe in OPTIONS: App Settings.)
  12. If you don’t see segments, make sure you have the check-boxes near the top set up so that the first four are checked, the next four are unchecked, and the pull-down has “All Sources” selected.
  13. If the import completed successfully and you have segments in the CHROMOSOMES tab, you can now close the GEDmatch window in your internet browser.  If the import did not work, try again using the Chrome internet browser.

Tips for Efficiency

  • You may have realized by now that you could have been running the GEDmatch Matching Segment Search in the background while you were importing the One-to-Many results into GMP.  Doing GEDmatch searches in parallel to GMP imports is a great time-saver.  Just be careful not to mix up profiles!
  • You don’t need to babysit the imports.  While one is running, have a cup of coffee, go for a walk, surf the ‘net … seriously, anything but sit and stare at the progress log!

 

In the next lesson, we’ll play around with the CHROMOSOMES tab in GMP. If you had any problems with this import, let me know in the comments.

 

Getting Started with Genome Mate Pro Series

6 thoughts on “Getting Started with Genome Mate Pro, Part 5 — First GEDmatch Imports”

  1. The 2nd phase of the import matching segment search gives a status line saying: “Triangulations Processed xxx of xxxx.” I wonder what GMP means here by “Triangulations” because it is impossible to compute triangulations from the segment match data that was just copied to GMP. Those are my matches to other people. There is no information in there to say that any other two people match each other on the same segment. Is GMP misusing the word triangulation?

    1. Tsk tsk, you’re getting ahead of me!

      You are correct that at this stage (first import for the first profile), there’s nothing to triangulate. That won’t always be the case, though. When you have more than one profile, GMP can actually calculate triangulations (true triangulations) on its own. For example, if you have a profile for yourself and one for your first cousin, and a third person triangulates with you, GMP can figure that out even if you never import triangulation data. That means GMP can do true triangulation of FTDNA data, as long as you have access to multiple profiles.

  2. Hi!

    Loving the series so far – very easy to follow. I’ve gone through Part 6, but the links for Parts 7-10 aren’t working. Is it me? Or is there a glitch in the series?

    Thank you!!!!

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