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: 

http://www.ctimls.com/Support/KB/Error%20Fixes/Fix_Silverlight_issues.htm

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

• http://www.microsoft.com/getsilverlight/get-started/install/default.aspx 

• http://www.ctimls.com/Support/KB/Error%20Fixes/Fix_Silverlight_issues.htm#Safari_7_Plug-in_Manager

Getting Started Guide

by George Cunningham

Some thoughts on starting to use Genome Mate

• Start with the videos: 

https://www.youtube.com/channel/UCc6l-LIZmND6MZv_EiA5-HQ/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:

http://genealogypuzzlesdna.blogspot.com/2014/03/using-chrome-tool-529andyou.html

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.