Using Genome Mate Part 3 (Importing GEDmatch Chromosome Browser Data)

The previous article in this series is Using Genome Mate Part 2 (Importing GEDmatch One To One Comparison Data).

Thanks to some great programming work by Becky Walker, the developer of Genome Mate, there is a new option for importing lots of match data at a time into Genome Mate, using Sue Griffith’s method of an alternate to the GEDmatch triangulation tool for locating shared segments with other testers (as also shown step by step in my last blog post). In this blog post, I will walk through the new Genome Mate import process step by step.

As shown in my last blog post, use Sue Griffith’s method to obtain a results page of shared segments in common with other people at GEDmatch, and then open up your Genome Mate software.

1) In Genome Mate, after making sure you have first backed up your database, select the profile for which you wish to add match data and click on the Import Data link in the menu bar near the top of the program window. (Note: the profile you are importing to must have the GEDmatch kit number of the profile person entered for the import process to work).

Using GEDmatch Step 4

2) Clicking on the Import Data link will bring up the Import Data window. Select the radio button next to GedMatch in the Select Data Source section, and then click on the (1) Load GedMatch Chromosome Browser Data link in the GedMatch Import Options section.

Genome Mate Screen Shot 13

3) Clicking on the (1) Load GedMatch Chromosome Browser Data link in the GedMatch Import Options section will bring up another Import Data window. Click once inside the rectangular box, and then switch back over to your Internet browser where you have the results page of shared segments in common with other people at GEDmatch.

Genome Mate Screen Shot 14

4)  On the GEDmatch results page, select everything on the page (Windows users hold down the Control key and press the A key on your keyboard, Mac users hold down the Command key and press the A key on your keyboard). Copy the data (Windows users hold down the Control key and press the C key on your keyboard, Mac users hold down the Command key and press the C key on your keyboard), and then return to your Genome Mate software.

Genome Mate Screen Shot 15

5) Back in Genome Mate, inside the rectangular box of the Import Data window, paste the data you previously copied from GEDmatch (Windows users hold down the Control key and press the V key on your keyboard, Mac users hold down the Command key and press the V key on your keyboard). Although the instructions warn that only the Chrome and Firefox browsers are supported, I have found that as of version 1.2.19 of Genome Mate, the Safari browser also works in most cases. After pasting your data into the box, click on the Format button.

Genome Mate Screen Shot 16

6) Clicking the Format button will bring up yet another Import Data window, showing the chromosomes and segments that are about to be imported. Before continuing, it’s always a good idea to make sure the profile listed is the one you want to import data to. After making sure you are importing to the correct profile, it’s also a good idea to take a quick look through the list to make sure everything appears ok. In the last column, in the Message field, you will see one of four things: a blank field, “Adding relative record”, “Duplicate match”, or “cMs below 7.0” (or the segment length threshold level you have set if you have entered something in place of the default value),

A blank field means the person you match with already has a record in your Genome Mate database, but this segment is new to your database and will be added. Adding relative record means the person you match with does not already have a record in your Genome Mate database, and they are being added to your database along with this segment data. Duplicate match means the person you match with already has a record in your Genome Mate database with this same segment data, so nothing additional needs to be added to your database for this segment. When it says “cMs below…”, it means the segment length is below the threshold level set in Genome Mate (7 cM by default, which is recommended), and this segment data will not be added into your database.

After reviewing to make sure there are not any obvious errors being reported in what you are about to import, click on the Add Data button.

(Note: If you get an error message saying “GedMatch Kit #s not found in pasted data,” check to make sure that you have selected the (1) Load GedMatch Chromosome Browser Data link and have not mistakenly selected one of the other options.)

Genome Mate Screen Shot 18

7) Clicking on the Add Data button will bring up the Import Summary window. This acts as a confirmation that the data was imported, as long as Matches Added and Relative records added are not both 0 (zero). If they are both zero, this is letting you know that something went wrong, and you should repeat steps 1 through 6 above. After verifying you do not have zeros for both Matches Added and Relative records added, click the Close button.

Genome Mate Screen Shot 17

8) Clicking the Close button returns you to the previous Import Data window, minus the Add Data button, and you can now click the Close button in the Import Data window.

Genome Mate Screen Shot 19

9) Clicking the Close button in the Import Data window will return you to the main Genome Mate screen. You can now begin working with your newly imported data, or go back through these steps to continue importing additional matches (for this profile, or for another of your Genome Mate profiles). Before proceeding, however, it is a good idea to do yet another backup of your Genome Mate database.

In the next post in this series, we will begin working more with the tools available in Genome Mate as we continue progressing towards generating a chromosome map of our DNA inheritance.

If you experience any problems while following these steps, or notice that a screen has changed from what I’ve shown in the screenshots, please let me know by commenting on this thread or sending me an email. Thanks for reading.

This article last updated 20 Oct 2014

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17 thoughts on “Using Genome Mate Part 3 (Importing GEDmatch Chromosome Browser Data)

  1. Pingback: Using Genome Mate Part 2 (Importing GEDmatch One To One Comparison Data) | Adventures In Genealogy Research: No Stone Unturned/The Wright Stuff

  2. Pingback: Steps to DNA Matching and Chromosome Mapping with GEDmatch and Genome Mate | Adventures In Genealogy Research: No Stone Unturned/The Wright Stuff

  3. I cannot get it to import my data. When I hit “Format” I get “Total import count: 0”
    I’m using Internet Explorer as my browser but other than that I’m following the directions exactly. Any ideas?

  4. Ok I figured it out! I had to use the Chrome browser to open and navigate thru gedmatch.com. If I use Internet Explorer it won’t copy (ctrl C) the page properly (it only copied the words, not the entire page, thus loosing the format). Then when I tried to paste the info into Genome Mate I would get the message about how it was an improper format. When I switched to Chrome it copied everything on the page, not just the words. And then it pasted and formatted properly. Sorry if this explanation is too long. I just wanted you to know why I had an issue and how I fixed it.

    • Thanks for your post and followup, Robin. I’m glad you were able to get your problem resolved, and the information you’ve provided will be helpful for others who may run into the same issue.

  5. Thank you, Dan. Wonderful series on GedMatch and Genome Mate. I was very excited to start working with my data (six profiles from my family). Unfortunately, I have experienced the same problem as Robin, i.e. improper format. Both Safari and Chrome will give this message. My own data on GedMatch is from FTDNA. I am following your directions to copy all in the One-to-many GM Chromosome Browser. Checking the data in the download window, before I press formatting, shows hat both the text and the tabulated data is there. After I press the Formatting, the error message appears. I have done it several times, including my sister’s data, after checking all settings. Same error message.
    What is wrong? I know that Gedmatch had some problems just about he time I was uploading.

    Béla Foltin

    • Hi Béla,

      Sorry to hear of your problems in trying to import data from GEDmatch. While I am unable to say for certain specifically what is the problem in this case, I highly doubt it has anything to do with the recent problems that the GEDmatch site was having. There are a couple things I can think of having you try in order to see if we can determine the cause of this particular issue:

      1) Have you tried doing an import of GEDmatch one to one comparison data? If not, please try to do so, and let me know if you have any issues getting the one to one comparison data to import.

      2) If you can import one to one comparison data without a problem, try to import the one to many comparison data again using Chrome, but this time in step 4 only check off the first couple matches, rather than checking off up to 200 matches. See if checking off only a couple matches makes any difference in whether or not you get the improper format error when going through the remainder of the steps. Please let me know what happens when you try this, and based on what you report we can try some additional things.

      Also, when replying to this, please let me know what operating system you are using on the computer you are using to generate the GEDmatch data and running Genome Mate on.

      I will await your reply,

      Dan

      • Thank you Dan,

        Gedmatch has been very flaky all day. All of my kits were usable before, but right now nothing works, neither one to one nor one to many in either Safari or Chrome. No criticism intended. I know that they have a monumental task and I have sent them support. They, and everyone in the DNA world has been very helpful. So, I could not perform, at this time, what you suggested. Instead, I tried to upload directly from FTDNA and DNAgedcom. They seem to have worked fine, although I am a little bit lost as to “what to do now”. I have read lot and am about half way through your series. I am brand new to all this, so it will take a little while; there is a lot of helpful material to read. Since I cannot produce any test results for you now, I have a couple of questions.

        I was wondering what are the relationships among the data from the testing companies, Gedmatch and DNAgedcom in terms of matches. I have not seen a clear statement about it. I am need the largest match pool because of some severe brick walls in my paper genealogy. Here is what I guessed: by using all three, one gets some new matches with each. So, what should the sequence be: load the test results into GedMatch, then load the Gedmatch into DNAgedcom (or reverse the last two?) and from there to Genome Mate.

        MY second question is regarding updating the data. I was told that In DNAgedcom one does not need to delete the old files; the new upload will overwrite them. In Gedmatch, one has to delete the previous uploads. What is the case in Genome Mate? I rather have the aggregate of the three match sources loaded, but, if need be, can one load them separately for each profile? How does one add new matches to the databases?

        I sense that Genome Mate is the ticket for me, since setting up spreadsheets is not my cup of tea 😖

        Currently I am running Genome Mate on my MacBook Pro (64bit) in in OS X Yosemite. Both Safari and Chrome are running. I usually access 23andme, FTDNA, GedMatch, DNAgedcom using Safari. Soon I will probably move all to my big screen Imac. I am too old to see detail on the small screen. I had no issues with Safari, but loaded and tried Chrome based on what I was reading in the blogs.

        Thank you for your help.

        Béla Foltin

        >

      • Béla,

        I also had some challenges with the GEDmatch site yesterday, and earlier today. It seems to be working much better now. Answering your questions:

        1) Yes, by using as many of the testing companies as you can you will increase the odds of helping you break down your brick walls. Unless I’m misunderstanding something in what you are trying to accomplish, there should not be a reason to have to load GEDmatch data into DNAgedcom (or vice versa) before bringing that data into Genome Mate. GEDmatch data can be imported directly into Genome Mate, and Family Tree DNA data can be imported into Genome Mate by using DNAgedcom to download the Family Tree DNA data. If I’m misunderstanding your question, please let me know.

        2) When you import data into Genome Mate, it will add new data if that data does not exist previously, and will update the data if the relative record already exists. The only thing I have found that you need to be careful of is if you have modified the name of an ancestor you previously imported via a GEDCOM, and import another GEDCOM containing that same ancestor. Any previously confirmed segments, with the ancestor whose name has been changed, will be lost and need to be confirmed again.

        Yes, I think you will really enjoy Genome Mate given that you mention spreadsheets are not your cup of tea. Even for people experienced with spreadsheets, I think they will find Genome Mate to be much easier to use for managing your data. In addition, the data can be exported from Genome Mate in spreadsheet format, for anyone who wants to do more detailed analysis in that fashion. Basically, the best of both worlds, in my opinion.

        Best wishes on your research,

        Dan

      • Thanks, Dan,

        I am totally impressed by Genome Mate! Since four of my six files are momentarily unusable at Gedmatch, I loaded up my six profiles from Dnagedcom into Genome Mate and the GEDCOM of my family tree, to boot. Everything works great, thanks to the fantastic software and your clear directions on how to do things. I have identified the possible ICW segments and now am ready to verify and triangulate. Since some of the files in Gedmatch that I need for one to one verification are not working, is there another way I can verify ICW matches and triangulate besides using GedMatch? I have about three blocks that are very promising in busting one of my worst brick walls in my tree: my paternal line, stuck at a marriage record in 1765. It looks as if Gaspar Foltin landed from Mars! I am even looking into triangulating Y-DNA (Roberta) by identifying rare marker values. I have not found a list of rare marker values yet. In he mean time, I am testing all the cousins that are still alive. Almost done.

        Thanks for your help. Some other questions are brewing in my mind, but will wait, maybe I will figure them out.

        Have a nice weekend.

        Béla >

      • Dan, I still do not understand the best path(s) by which I can bring all the possible matches into Genome Mate, i.e. from all sources: FTDNA, DNAGedcom and GEDmatch. Do I separately load files from each of these into my profile in Genome Mate, which then picks and adds new matches from each upload? Or, is there another process?
        I have seven profiles in GM directly loaded from FTDNA, but of course I miss out on matches that would be found only on DNAGedcom and Gedmatch. For example matches that come from Ancestry or 23andme etc.
        Thanks.

        Béla

      • Sorry to have taken so long to reply, Béla. I have seen you posting on the Genome Mate Facebook page, so I’m hoping you have found your answer there. If not, or for the benefit of others who may come across your question here, each source needs to have it’s own import done, unfortunately. DNAGedcom has introduced a tool, however, which is able to handle most of the downloads from the various testing companies, so I would certainly encourage you to take a look at that, if you haven’t already. Hope all is going well with your research!

      • > Thanks Dan. I sort of figured things out. At the beginning, I was confused about what to load to the different “tools” (Gedmatch, Dnagedcom) and how to supplement the uploads when new matches appear at the source site. Gedmatch is a one time raw data load, unless something changes about the raw data. It does not involve matches at the source. Dnagedcom and Gedmatch requires replenishing as new matches appear at the source site. Right now I am “baby sitting” the download of the full match data from my new kit at Ancestry using the wonderful automated Chrome extension by Jeff Snavely, Ancestry DNA Helper. It is slow, but can be interrupted. When restarted, it continues where it left off. I am on day two of the download, but not complaining 😃 > Next I will be downloading my 23andme data to Genome mate with another Chrome extension. > Thanks for your help. > > Béla

        >

  6. Dan,
    I can’t seem to find the answer. .Genome Mate sent warning that db is too full and I should either separate profiles or delete the smaller matches. I choose to delete the matches smaller than 9cM as well as duplicate records but cannot find a way to do this. I am using the original Genome Mate program.

    Thanks for your help

    • Hi Barbara,

      After making sure you have made a backup of your database, to delete the matches smaller than 9 cMs, go to Options > Database Cleanup. In the box at the top center of this window, enter 9 in the Remove Options Minimum cMs: box; then in the Remove DNA Match Segments section, select the data source, click to put a check in the box for Where cMs is less than minimum and then click the green Remove DNA Segments button. Repeat these steps for each of the different data sources you are using within Genome Mate. You will also see options within the Database Cleanup screen for other things that may help reduce your database size.

      Alternately, please be aware that Genome Mate Pro does not have these same database size restrictions, so upgrading to GMP would also resolve the issue, and would be the best thing to do if you want to maintain the segments smaller than 9 cMs that you currently have in your Genome Mate database.

      Hope this helps, but if my instructions don’t make sense, or you get stuck on any of the steps, please let me know.

      Best regards,

      Dan

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