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

• 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