Friday, March 28, 2014

Getting Started with Genome Mate

Genome Mate is a desktop tool used to organize in one place the data collected while researching DNA comparisons.  Besides data storage it has many features to aid in identifying common ancestors.  It can be downloaded at http://genomemate.org/



The following guide was put together by George Cunningham and published here with his permission.  But first a few technical details that you can skip if you have Genome Mate installed.

Browsers

Genome Mate is written in Silverlight/C# and I have tested it on Chrome, Firefox and IE browsers on a PC.   Firefox seems to work best for installing the application on a Mac per user feedback.

Chrome is the recommended browser for every day use as the 529andYou addon is available and it works well with  DNAgedcom.com downloads.

Silverlight

The application is usable by both Mac and PC users but there are incompatibilities with some Mac OS that cause a crash when using a link within the application.  I have code in the application for a soft landing when an unknown error occurs but this is happening outside the application. For a possible solution see: 


These links will give more information on what browsers and operating systems are supported by Silverlight. 


Getting Started Guide

by George Cunningham

Some thoughts on starting to use Genome Mate

  • Start with the videos: 
  • First create a profile in Genome Mate  
    • Profiles > Add new profile
  • Put in a name, any name will do, but
    • You are a good choice for the profile person.  
    • If your going to use data from 23andMe for the profile person, the profile name MUST match the 23andMe name.
    • I also have my sister on a separate profile as I have FTDNA data for her.
    • I will add my uncle as a profile person when I get his FTDNA results
    • One profile is good to start.  It is easy to add others once you know the drill.
  • Load a gedcom file for each profile if you have one.  If not just continue.
    • The gedcom file can be all of your relatives and more
    • Genome Mate will ask you for the name to associate with the profile person, and will strip out all but the profile person's direct ancestors.

Data Sources


  • There are three main sources of data:  FTDNA, 23andMe, and GedMatch.  
  • You can download in any order.  I prefer FTDNA first because I get the most data for the least effort, then 23andMe, and finally GedMatch.
  • If you have known relatives tested on 23andMe, it makes sense to do 23andMe first.

FTDNA Data Upload

  • From Genome Mate do 3 uploads of data:
  • Import Data > Select Data Match Source > FTDNA Family Finder Chromosome Browser CSV file
    • Follow the directions for downloading the CSV file or use file from DNAgedcom
    • Upload it to Genome Mate following the directions from above.
    • This is the actual DNA data.


  • Import Data > Select Relative Data Source > FTDNA Family Finder Matches CSV file
    • Follow the directions for downloading the CSV file or use file from DNAgedcom


    • This has other useful information like the contacts email address which will be automatically associated with the relatives record.
  • Import Data > Select Relative Data Source > DNAgedcom: ICW CSV file.
    • The ICW file is worth doing.  
    • Just be aware it can sometimes take several hours for DNAgedcom to generate it. 
      •  dnagedcom.com > Family Tree DNA > Download Family Tree DNA Data
      • If things don't work out, DNAgedcom support is very helpful.

23andMe Data Upload



  • From Genome Mate you will do two uploads of data.
  • Before you begin, learn about the 529andYou Chrome Browser add in. Here is a tutorial:


  • Do one comparison in 23andMe > My Results > Family Inheritance: Advanced > Compare > View as Table
  • Then open the 529 tool from the browser search bar and 
    • Create 'To Do' Table


    • Click each Compare button.  

      • It will open a new tab, but you do not need to look at it.


    • When all the Compare buttons are done
      • If there is more than one 23andMe profile, switch profiles do the To Do again
      • Close the 529andYou tab
    • Open the 529 tool from the browser search bar again to pick up new relatives


    • Set Display Mode to Profile and Overlapping Segment Links
    • For each new Relative
      • Select {name} in "Show matches of"
      • Click on Create Match Table
      • For each match displayed
        • Click on Show Overlapping Segments button
        • If any, Ctrl Click on all "compare {name} and {name}" links
          • This will show them in a separate tab
          • When each tab is complete, just close it
        • Click on Create Match Table to do the next match
      • Select All in  "Show matches of"
      • Download CSV
  • Back in Genome Mate
    • Import Data > Select Match Data Source > 529 and You: 23andMe FIA CSV File
      • Select the 529 CSV file that you just downloaded.

GedMatch Data Upload

  • From Genome Mate you can only do one bulk upload.
    • In Genome Mate > Import Data > Select Match Data Source > GedMatch: Segment Triangulation
      • Follow the directions
    • In addition, you can do one by one uploads Import Data > Select Match Data Source > GedMatch: 1 to 1 Comparison.
    • You need to transfer the names from GedMatch to the Genome Mate relative record manually. 
      • This is painful, but the format of the GedMatch one to many file makes it impossible to get the names and emails automatically. 
  • My procedure for adding names to GedMatch relatives is:
    • Do a one to many on your kit in GedMatch.
    • Back in Genome Mate, left click the relatives Match Key to bring up the person's editing box. 
    • Right click the Match Key to copy it to the clipboard.
    • Search the one to many screen for the Match Key.
    • Copy and paste the name into the Relative Box.  
      • I like to keep the match key so it displays on the main screen, as in Joe Jones (F123456)
    • Copy what you can of the email, paste, and fill in the rest manually.

Hints and Tips

  • There are two small arrows going in a circle to the left of your profile name. Left click.  Escape to return to the original screen.


  • Choose a Relative Name in the list of matches.  

    • Choose one who matches you on more than one chromosome. 
    • Right click on it.  
    • Esc to go back.
  • Some Relatives will have a small symbol (Mark ICW segments) to the left of their name.   Hover (do not click) your mouse over the symbol.
    • A series of colored bars will show you the relatives who have "in common with" the one you are hovering over.  
    • These people are related but necessarily on the currently selected segment.


  • Some ICW group symbols are in orange.

    • The orange color means that the segment crosses a centromere, so the meaningful length is much shorter than the displayed length.  
    • If you hover over the symbol, it will show the length of the centromere. 

Backups & Restores 

The words of wisdom on creating backup files cannot be overemphasized.   Once you have all of the CSV files downloaded and saved, it only takes a few minutes to redo.  So experimentation is encouraged, but make sure you have a safe harbor.
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Sunday, March 16, 2014

Using the Chrome Tool: 529andYou

It has been a while since my last post.  I intended to document my journey through the exploration of DNA genealogical research but that journey has been so fascinating that I was completely distracted by oh so many things.  In the mean time, I have confirmed some of my ancestors whose documentation was sketchy, broken through one brick wall and have clues for breaking another down.

However, the purpose of this post is to describe how to use one of the best tools around for collecting 23andMe data, the Chrome addon 529andYou by Roger Woods.  If used correctly, not only will it retain match data but it can be used to identify in common with (ICW) data for each relative.

1.  Skip this step if you already have the Chrome browser.  Click here to get Chrome.

2.  Click here to get the 529andYou Chrome addon.  Be sure to select yes to create a database when asked.

3.  Open 23andMe to Family Inheritance: Advanced and select two profiles.  Then click Compare and when the results are shown, click on View in a table.  In the upper right corner, you will see this icon.   Click on the icon to open the 529andYou tab.


4.  Next click on the Create 'To Do' Table button and for the profile you have selected in 23andMe, it will display all matches for which data has yet to be recorded.


5.  For each match, click on the Compare button and 529andYou will open a tab to the 23andMe FIA page to get the comparison then record it in it's database.

6.  To see how each person compares to each other, close the 529andYou tab then reopen it from the FIA page.  Select display mode "Profile and Overlapping Segment Links".  Click on Create Match table.


7.  Click on the Show Overlapping Segments button for each match, one at a time.  In the resulting table, click on the compare links under each Show Overlapping Segments button.  Use Ctrl click or Cmd click to open each in it's own page.  This will load the comparisons into the 529andYou data base.


Now the data is loaded and can be viewed within 529andYou by selecting a name and chromosome.

I use this tool for 23andMe data collection every week or so then download the data into a CSV file and import it into Genome Mate.  For each profile I have in Genome Mate, I select the profile name and click on the Download CSV file.  Then I select Show matches for All and download a CSV file that I use to update ICW for 23andMe matches in Genome Mate.

If you have a lot of relatives on the list, it takes a while to update the database the first time but it is well worth it as later it only takes a few minutes to get updates when new sharing invitations are accepted.  Of all the ways of collecting 23andMe data, this is my tool of choice.

~ Becky ~
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