Getting Started with Genome Mate Pro, Part 7 — More GEDmatch Imports

Scroll down for links to other posts in this series.

The GEDmatch Matching Segment Search import that we did left us with some holes in our segment data. Specifically, it didn’t import data for close relatives, nor did it import segments for people who only match on the X chromosome. Today, we’re going to learn about some new types of import to get that information. If you’ve made it this far, we know your profile is set up correctly for GEDmatch, so we can speed up a bit.

First, we’re going to use the GEDmatch one-to-one import to get segment data for a close relative (parent, child, full sibling). If you haven’t tested anyone in that category, pick your next highest match so you can follow along.

I recommend using the Chrome internet browser for GEDmatch imports.

 

Run a “One-to-One Compare” Report in GEDmatch

  1. In your internet browser, log into GEDmatch and do a one-to-many search for your kit. In the “Details” column, click the blue “A” for your top match to get to the one-to-one comparison entry form.
  2. On the entry form, make sure the radio button for “Position Only” is checked, then click SUBMIT at the bottom.
  3. Select and copy everything on the next page. (control-a then control-c on a PC; command-a then command-c on a Mac).

 

Import the “One-to-One Compare” Report into GMP

  1. Open GMP.  In the File menu, select Backup Database. Get in the habit of doing this before every import.
  2. Click IMPORT DATA in the menu at the top of the screen, then “From GedMatch”, then “3: 1 to 1 Comparison (optional)”.
    Click OK to dismiss the pop-up that appears with instructions on how to acquire the data. (We’ve already done that.)
  3. Click the PASTE button at the bottom left of the next pop-up to insert the info you copied from GEDmatch. Click IMPORT at the bottom right.
    Don’t worry about the skipped lines indicated at the bottom.  Notice how quick this import is!
  4. Review then close the pop-up that summarizes the import.
  5. If this person was a parent/child/full-sib, you should now see their segments in the chromosome browser. If this person wasn’t in that category, you’ve probably just re-imported data you already had, and GMP will ignore it. No harm done.
  6. If you have more close relatives tested, do the one-to-one import for each of them.

When would you want to use the one-to-one import? I’ve already shown you that you can use it for a close relative that was skipped by the Matching Segment Search. I also use it when I get a new, promising match at GEDmatch and I’m too impatient to do the full suite of imports. You might also use it if you want to see quickly whether two of your matches also match one another (that is, whether they triangulate with you), in which case you’d import a one-to-one between their two kit numbers.

 

Collect Segment Data for the X Chromosome in GEDmatch

  1. In your internet browser, log into GEDmatch and select the one-to-many search.
  2. Enter your kit number, select the radio button for the X chromosome, set the pull-down for cM limit to 10, then click the DISPLAY RESULTS button.
    Note that the default threshold for importing X segments into GMP is 10 cM, so unless you’ve lowered that setting, there’s no point in searching for X segments shorter than that.
  3. In the “Select” column on the next page, check each box for your top 10 matches. (NOTE: If you’re male, you may have fewer than 10 X matches. In that case, select them all.)
  4. Click the SUBMIT button towards the top of the GEDmatch page.
  5. On the next page, click the CHR-BROWSE button beside “2-D Chromosome Browser” (not the 3D Chr-Browse one).
  6. On the next page, click the blue HERE link.
  7. Select (control-a or command-a) and copy (control-c or command-c) everything on that page. Do not close the window

 

Import X Chromosome Segment Data into GMP

  1. Open GMP and back up your database.
  2. Click IMPORT DATA, then “From GedMatch”, then the oddly named “2: Import Chromosome Browser data via Chromosome Browser Data”.
    Click OK to dismiss the pop-up with instructions.
  3. The next pop-up asks whether you want to import that data into the profile listed. Double check that you ran the right GEDmatch chromosome browser search for that person, then click YES.
  4. In the next pop-up, click PASTE then IMPORT.
  5. Review then close the pop-up that summarizes the import.
  6. In the Chromosomes tab, switch to Chr: X and behold your lovely segments. Assuming it’s been a few days since your first imports into GMP, the newly added segments will be highlighted in yellow.

 

Some thoughts on this import: If you had fewer than ten X matches, you’re done. If you had more and want to import them, you’ll have to repeat the chromosome browser import steps described above in batches of about 200 matches. GEDmatch has a limit on how many kit numbers you can run through their chromosome browser at once. If you select too many, you’ll get an error when you click the CHR-BROWSE button in GEDmatch. You’ll then have to back up, uncheck some, and try again.

If you can’t afford to pay for the Tier 1 tools at GEDmatch, the chromosome browser import is your workaround in place of the Tier 1 Matching Segment Search import. You’ll have to work through your matches and import them in groups of about 200.

TIP:  There is an extension for the Chrome internet browser called “CheckChrome” that allows you to select multiple rows of text on the screen and check all of the boxes therein by right-clicking.  If you are comfortable installing extensions on your internet browser, I highly recommend it. Be aware that CheckChrome may take several seconds to check 100–200 boxes.

Getting Started with Genome Mate Pro Series

 

Please follow and like us:

18 thoughts on “Getting Started with Genome Mate Pro, Part 7 — More GEDmatch Imports”

  1. Leah: You say “You might also use it if you want to see quickly whether two of your matches also match one another (that is, whether they triangulate with you), in which case you’d import a one-to-one between their two kit numbers.”

    Okay, but then what do we do with that in GMP. We can’t add them to our own profile since they aren’t our own matches, or can we?

    1. We’ve seen four imports so far, and three of them give you a pop-up asking if you want to import that data into the active profile. The one-to-one import doesn’t ask, though. That’s because GMP isn’t associating the import data to the profile by default. Instead, it’s able to pull the GEDmatch numbers from the text itself. If one of those GEDmatch numbers happens to be the same as the “match key” for the profile person as set in the Profiles tab, GMP can figure that out. If not, GMP stores the shared segments as between two other people. If you match each of those other people in the same place they match one another, GMP will infer the triangulation all by itself!
      (Skipping ahead, the GEDmatch Triangulations import works similarly in that it’s not tied to a particular profile.)

  2. Hi Leah – this is a great series!! In the past I had avoided GMP because something in the developer’s notes had given me the impression that software was inherently unstable. Your series here gave me the push to try it, and I am glad to report that it all seems to work quite well!

    I did not realize that the matching segment search tool in GEDMatch does not return segments for people who only match on the X chromosome (i.e. those were autosomal cM = 0). Now that I know where to find them, I have 3-fold more X-segments to play with!

  3. I appreciate these tutorials so very much! This is just what I needed. I had attempted to use DNAGedcom, but felt overwhelmed and so I was afraid to even try GMP. I am so glad you took the time to do this.

    But I am having a little trouble with the X matches. I have a ton and it is very tedious clicking on each check mark. So I installed the CheckChrome extension, but can’t figure out how to make it check all the boxes. I am highlighting multiple rows and then right clicking and selecting “CheckChrome” and then the option “check” but nothing happens. Any thought?

    Can’t wait to move on to Part 8.

      1. Glad to hear! Sometimes it takes the CheckChrome extension several seconds to “check” the boxes when you select a lot of them.

  4. G’Day
    I’m really enjoying all this series, have always been daunted by keeping spreadsheets up to date for 14 kits, so this is a godsend :).
    My next question for you (sorry)………
    I have noticed with the X DNA imports from GEDmatch that the SNPs have not come through. There are some existing matches already under the X column and these have SNPs. Looking at your example the yellow line addition has 0 SNPS also……is this normal or have I have not completed a step somewhere?

    1. Yes, it’s normal. Data imported through the chromosome browser at GEDmatch does not have SNP data. If you really want it, you’ll have to do one-to-ones.

  5. You say to check the first 10 boxes under “select” for collecting segment data for the X chromosome. However, I’m the top 2. Should I still click them? or start with the first one that’s not me?

  6. Leah, fantastic write-up, love the step by step. I had a question about marking the side for nieces and nephews and their descendants. Are they “B = both?”

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.