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

June 11, 2018 43d Comments

Scroll down for links to other posts in this series.

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

 

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43 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?

    Reply

    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.

      Reply

  3. 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!!!!

    Reply

    1. Part 7 hasn’t been posted yet. I’ll try to have it up by tomorrow morning. Thanks for the nudge!

      Reply

  5. I’m pretty sure I followed the directions for Matching segment search, but it is completing without the end positions which leaves me with no information. It also is not showing the countdown of imports as it did for the one to many. That imported successfully. Perhaps there’s a glitch in my browser (Chrome).

    Reply

    2. I am having the same issue. I have tried it multiple times and getting the same result. It does appear to be a different version on gedmatch, so I’m not sure if that is the issue.

      Reply
  7. Pingback: Getting Started with Genome Mate Pro, Part 3 — Activate GEDmatch Import Templates – The DNA Geek

  8. G’Day

    Loving this series, thank you so much for getting me started with GMP!!!

    I have a question re GEDmatch, I see that the default setting for the ‘One to Many Matches’ is the Generation range and this is what I imported to GMP as per your post.
    This option showed my estimated Generation range from 1.0 to 5.8 and the cM totals were mixed throughout the search.

    I decided to search from Total cM and this went from 3587.1 to 12.7, the latter having a generation range of 7.1. This indicates that not all my matches were displayed in the original search as the Generation range only went to 5.8.

    Therefore I can’t be copying all my GEDmatch matches to GMP and I have heard (sorry, can’t recall where or when) that with GEDmatch regular you only see your first 2000? matches.

    The 7.1 generation with 12.7cM/7.0 Longest Block might be just as valid as the 9.5cM/9.5 Longest Block at 5.8 Generation range and when it comes down to it the Generation range is estimated based on the perimeters each company uses, although I guess in this case the Longest Block has been used in factoring the order.

    My question is how do we see all our GEDmatch matches and how do we copy them all to GMP for assessment with GMP tools?

    Thanks in advance 🙂

    Reply

    1. The One-to-Many import doesn’t pull in segment data, only ancillary information like names, email addresses, and haplogroups. (And technically, there are other ways to import name and email address.) So, I wouldn’t worry about differences in how the report is sorted.

      That said, I don’t know of any way to see *all* of your matches at GEDmatch in a single search. Even the Matching Segment Search won’t pull them all in. You’ll have more than you can ever work with using the imports we do, though!

      Reply

  9. Wow! This is wonderful. Just completed Part 5. Was about to ‘ask a question’ when I read the opening of Part 6 which answered the question. You are doing a great, thank you, thank you.
    Nancy

    Reply

  10. Question: Do I have to Import Templates for each Profile I create? Or can I just do this once?
    All of my test kits are from Ancestry. I have downloaded the RAW DATA from Ancestry into GEDmatch.
    When I change between PROFILES the IMPORT TEMPLATES I first activated are ‘dark fonts’ which I take to mean they are ACTIVE for this PROFILE. Is this a correct assumption?

    Reply

    1. You only need to activate templates once, and they’ll be available to all of the profiles in that database.

      Reply

  12. I spent a few minutes on the first task in Part 5 but I guess I am pretty dense because I tried various means to try to select a ‘side’ for a couple of my 1st cousins listed and I could not get it to work. I guess I didn’t understand what I could or had to do to make this happen. .

    Reply

  14. Following your instructions I used gedmatch to import my ancestry kit matches into GMP. Can I repeat the same procedure into the same GMP profile but using my 23&me kit on Genesis? Will I end up with a bunch of dupe? Wondering if I should have just used genesis from the start since regular gedmatch doesn’t pick up my 1C 23&me kit.

    Reply

    1. GMP uses the GEDmatch kit number as a unique identifier, so you shouldn’t get duplicates caused by importing your Ancestry kit from Classic GEDmatch and your 23andMe kit from Genesis. Note that a lot of people have duplicate kits (with different kit numbers) at GEDmatch, and those will appear as duplicates in your GMP database, but that’s not a function of you importing twice. Those duplicates will appear even if you only import one of your kits into GMP.

      Reply

      1. Thanks for the fast reply! Walking through your instructions now for GMP and I swear you are saving me about a year of learning. Couldn’t be more grateful. Maybe I can finally figure out this missing 1C level connection. 🙂

        Reply
  15. Pingback: Getting Started with Genome Mate Pro, Part 1 — Install the Program – The DNA Geek
  16. Pingback: Getting Started with Genome Mate Pro, Part 2 — Set Up a Profile for a GEDmatch User – The DNA Geek

  17. First of all thank you very much for taking the time and trouble to explain how to use Genome Mate Pro for non tech users. I’m so grateful. I am determined to master all things genetic genealogy as I find is fascinating and it also has the added benefit of giving my aging brain a good workout!
    I seem to have hit a problem. I think that I have successfully downloaded my relative list from Genesis Gedmatch Tier 1. The problem has arisen when I tried to download the segment matches. The matching segment search gave me 2284 segments but 1927 of these were skipped. Looking at the relative list, most do not have any segments recorded and in the remaining other cases the number of segments recorded is incorrect. For example for one 2nd cousin Genome only has the segment details recorded for Chromsome 2,6,9 and 12 but in Gedmatch we also have matching segments (well over 7cM) in Chromosomes 7, 8, 15 and 17.
    Any advice on how to correct this, greatly appreciated.
    Kind Regards
    Anne

    Reply

    1. I do not recommend importing Genesis matches at this time. There are still a lot of glitches in the matching system there. For now, I suggest you stick with regular GEDmatch and, if you have an important match at Genesis, import them through a one-to-one.

      Reply

  18. Following up from my last comment. I have found out where I was going wrong. The minimum SNPs for imports was at the default setting of 700SNPs. I changed this to 350SNP and had 1135 segments skipped as opposed to 1927 segments previously.
    Do you think that 350SNPs is too low?
    Thank you,
    Anne

    Reply

    1. I’d like to piggyback on this question. Doing a one to one comparision at GEDmatch, I noticed the following message:

      “Segment threshold size will be adjusted dynamically between 200 and 400 SNPs
      Minimum segment cM to be included in total = 7.0 cM”

      It seems to me before the events that lead to the revised GEDmatch (merging functionality first introduced under Genesis), the minimum SNPs had been higher, though I could be wrong.

      For GMP imports, I had been using a setting of 550 SNPs. I’m considering lowering the SNPs threshold to be consistent with what GEDmatch now uses as the default for determining matches. I’m interested in your thoughts on this.

      Reply

      1. Yes, GEDmatch has lowered the threshold to be able to compare kits that were tested with different chips that have low SNP overlap. Personally, I err on the side of caution and use a minimum of 500 SNPs.

        Reply

  19. Can’t find or see “Import Data menu” after opening CHROMOSOME TAB in STEP 5.

    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.
    Using the Import Data menu, select “From GedMatch” then “1: Create Relatives Records via One to Many Matches”.

    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.
    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.

    Reply

  20. I found the “Import Data menu”, but clicking on “From GedMatch” then “1: Create Relatives Records via One to Many Matches”, does not give pop-up instructions on for how to collect the data from GEDmatch,or a button todismiss it.

    Reply

  21. Import One-to-Many Data into GMP. When I click on “1: Create Relatives Records via One to Many Matches” no pop-up shows giving instructions for how to collect the data from GEDmatch. As a result of that pop-up not showing, no other pop-ups show.

    Reply

  22. Have tried several times to download one to many matches, and used the useal Gedmatch one to many, and the BETA which gives more info. In eithercase within a minute it stops and says not enough fields 39 and thats it, incomplete cannot get data into my profile?

    Reply

    1. You’re probably using the wrong one-to-many report. GEDmatch has several now that have very similar names, and the output can vary depending on whether you have a Tier 1 subscription or not (even if you’re running the one-to-many that doesn’t require Tier 1). Make sure you follow the pop-up directions in GMP very carefully.

      Reply

  25. Ignore my last comment! Sorry. I “panicked too soon”. There are *some* names. But *most* of them were simply listed as “A”.

    Reply

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