Friday, September 19, 2014

Genome Mate: 23andMe Ancestry Composition

There's a new feature in Genome Mate that will allow loading of the 23andMe Ancestry Composition (AC) file from DNAGedcom into Genome Mate generation zero base segments.

Step 1:  Download or Create AC File

The Ancestry Composition file can be downloaded from DNAGedcom or created manually.
  • DNAGedcom:  On> 23andMe > Download 23andMe > Enter Email address > Enter 23andMe Password > Enter 23andMe Profile Name >  Check Run AC > Get Data and wait for it to finish processing
  • Manually Created File:  DNAGedcom is the preferred method of getting this data formatted correctly but a comma separated values file with similar data will also work or the AC file from DNAGedcom can be edited prior to import into Genome Mate to include just the desired segments.  Sample format:
Chr, Origin, Bar, Start, End, Level
Chr:  This is the chromosome number.  Note how X is formatted differently
Origin:  This is the label to use on the Segment
Bar:  1 is maternal, 2 is paternal
Start:  Segment start point
End:  Segment end point
Level:  This is the how the segment is to be layered with 1 being to bottom layer
Save the file as a CSV file (i.e. file name is {something}.csv) 

Step 2:  Import AC File

Every time the AC file is imported it will replace existing AC or generation zero segments. 
In Genome Mate > Import Data > Select Match Data Source: 23andMe > Load Ancestry Composition Segments > Select Profile Name > Select file named {email name}_{profile name}_23andMe_AC.csv

Step 3:  Set Option

Since the AC data can clutter up the display, the ability to toggle it on/off is included as an option.

In Genome Mate > Options > Check Show Ancestry

Step 4:  View Segments

AC segment data will automatically be displayed on the main page chromosome map but may be covered by segments defined from DNA matches.  Open the Segment List to see the Ancestry segments for all chromosomes:

In Genome Mate > Segments > Check Ancestry

Hovering over a segment will show it's origin.

Step 5:  Changing Colors/Swapping Bars

Since the AC bars are not defined as maternal or paternal at 23andMe, they are randomly assigned to bar 1 or 2. If through data analysis, it becomes apparent that they are reversed, the bars can be switched.  On the reversed chromosome, right click on an AC segment then click on the swap icon next to the segment color selection.

Finally note that the matches contained within an AC segments can be view on the main page by checking the Segment box.


Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014

Wednesday, September 10, 2014

Genome Mate: Segments Option

In Genome Mate, a segment is defined as a slice of DNA associated with a set of ancestors for the current profile person selected.  Segments are a way to defined what DNA for the profile person was inherited from which of their ancestors.

Let's first describe how to set up segments then move on to the Segments Map.

Creating Segments

Segments are created automatically when on a Match Details page, the ICW is set to start with M for maternal or P for paternal, AND the confirmed ancestors (MRCA) for that match are selected.

This creates a temporary segment that will be shown on the chromosome map at the top of the main page and on the Segment map.  Note that confirmed ancestor selections are only available if a gedcom has been uploaded for the profile person (Profiles > Select Profile > Load Gedcom File).

To view segment information, on the Main page, right click on the segment on the chromosome map and the Segment Details page will be displayed showing the surnames associated with those ancestors and the matches that were used to create the segment.

Segments Detail Page

A temporary segment is created when setting the ICW and confirmed ancestors on the Match Details page.  If that information is changed in the Match Details page, then the temporary segment will also change.  

When you are confident of a segment's definition, make it permanent by clicking on the Save button and you will be given the option of naming the segment id and marking the ICW of other associated segments with the segment id.  You may also add comments to the segment description.

Use the Delete button to remove permanent segments no longer wanted.

Segments Map

Segments Map
To access the Segments Map, on the Main Page click on Segments.  This displays the segments for all 23 chromosomes in either a map or table format.  To manually add a permanent segment, click on the Add Segment button and fill in the information.

There are times when mapping an ancestor is desired but intervening ancestors are not known as in the case of adoptees or in trying to push through a family tree dead end.  Adding a manual segment allows for the identity of the known segment.

Final Comments

Some thought needs to be given to how to use permanent segments and how to assign segment ids.  It took me several attempts to settle into what was acceptable for my data.

It is recommended that you backup your database and experiment before settling on a particular course of action.


Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014