Go Back   Family Tree DNA Forums > Universal Lineage Testing (Autosomal DNA) > Family Finder Advanced Topics

Family Finder Advanced Topics Advanced discussion about Family Tree DNA's Family Finder Product.

Reply
 
Thread Tools Display Modes
  #1  
Old 25th July 2014, 11:34 AM
tlgarrison tlgarrison is offline
FTDNA Customer
 
Join Date: Jul 2014
Location: Illinois
Posts: 132
Trace or Minor Admixture percentages

A lot of us have some Native American admixture. Some of us (not me) know where this comes from. Some of us have the stories handed down etc about their great grandmother/father etc. So when you get the Native American percentages you have a good idea where it comes from.

Our family had no such stories but grandmother said she just knew there Native Ancestry because of some of her features.

I started thinking about a way to try to isolate the line or lines that contributed this to my family.

I am thinking why not use GedMatch admixture with chromosome painting (I always save my results from Gedmatch so I still have them). Using the chromosome paintings, highlight the areas on each chromosome that are Native American, SE Asian, etc.

Then using that information and the chromosome browser try to determine the people that are matching along those segments that align with those minority admixtures.

This was getting way to tedious with doing only 5 at a time in the chromosome browser. It worked a little better in Genome Mate. But I want to visualize the minority admixture on the screen overlaying the segments of all chromosomes at once and all my matches at once.

So my next venture is to export my chromosome browser matching segments and digitize my minority admixtures and create an application to display them together in one huge chromosome browser and see if I can see any patterns with those minority admixtures and my matches.

Does anybody see a problem with this workflow? I have my matching segments downloaded and wrote the code to bring them into a grid sorted by chromosome, start and stop locations. So I need to draw the matching segments to scale and then add the minority admixture from my chromosome painting.

Hopefully in a couple days I can upload an image of the results from this endeavor (good or bad).
Reply With Quote
  #2  
Old 26th July 2014, 11:58 AM
tlgarrison tlgarrison is offline
FTDNA Customer
 
Join Date: Jul 2014
Location: Illinois
Posts: 132
I hit a little snag as I was working out the logic. My mother does not have Native American and since I don't have my father's results back yet, I need to be able to remove my mother's matches from my list. This should (theoretically) give me only my father's results. I guess since I have colonial lines on both sides, then this might remove some matches that are common to both.

So I will load my matches, then flag all my matches where she also has matches and call those maternal for now. Then I should be able to filter and turn that off or on to see all or just paternal side.

I am attaching a screen shot of my progress so far. I was able to load and sort my matching segments by chromosome, start, name and then I calculated some stats (just garbage for now) and display the #of SNPs and Centimorgans. I am going to add a check box field that will be checked if it matches my mother. But for now I just had the application color my name pinkish to show me that that is a maternal line match. I also blocked out portions of the names for privacy. I colored all matches a common color if they had a significant overlap.

Now I should be able to create the chromosome browser portion.
Attached Images
File Type: jpg project.jpg (147.6 KB, 15 views)
Reply With Quote
  #3  
Old 27th July 2014, 07:45 AM
tlgarrison tlgarrison is offline
FTDNA Customer
 
Join Date: Jul 2014
Location: Illinois
Posts: 132
Chromosome Browser with Admix

This was not as hard as I thought it would be. I created a text file to hold my minor admixtures, Native American (orange), SE Asian (bluish color). I also entered the poor SNP regions (Grey) and the centromere (yellow vertical line) for each chromosome.

I had the program plot each of my matching segments (5 cM or greater) along with their name, cM value and (SNP count).

I then use the Native American admixture to see if I see a pattern (following certain segment matches).

The area where I have the most Native American, chromosome 9, was empty of matches! But I did see a pattern on a couple other chromosomes (2 and 13). I also have these segments worked out. They are my Skaggs family segments. They were known as Long Hunters. See attached images. PS. Sorry I did not highlight area of chromosome 2 before I uploaded it. It would be the white segments.
Attached Images
File Type: jpg Chromosome2.jpg (92.2 KB, 15 views)
File Type: jpg Chromosome13.jpg (102.4 KB, 7 views)
File Type: jpg Chromosome9.jpg (211.3 KB, 4 views)

Last edited by tlgarrison; 27th July 2014 at 07:52 AM. Reason: added P.S.
Reply With Quote
  #4  
Old 28th July 2014, 11:27 AM
Canyon Wolf Canyon Wolf is offline
FTDNA Customer
 
Join Date: Feb 2014
Posts: 52
Interesting Project

I tried to do the same thing last year and gave up because it was too time consuming and I wasn't sure if it would actually tell me anything when I was done.

Do you plan to offer your tool to the public at some point?
Reply With Quote
  #5  
Old 29th July 2014, 12:33 PM
tlgarrison tlgarrison is offline
FTDNA Customer
 
Join Date: Jul 2014
Location: Illinois
Posts: 132
Quote:
Originally Posted by Canyon Wolf View Post
I tried to do the same thing last year and gave up because it was too time consuming and I wasn't sure if it would actually tell me anything when I was done.

Do you plan to offer your tool to the public at some point?
Maybe when I get some time to clean it up a little. Right now it is all directly wired to my results. I need to make it so the user can select which results they want to analyze. Also, it takes a little explaining on how to create the minority admix text file.
Reply With Quote
  #6  
Old 31st July 2014, 06:35 PM
Canyon Wolf Canyon Wolf is offline
FTDNA Customer
 
Join Date: Feb 2014
Posts: 52
Beta testing volunteer ;-)

If you are still working on this project after the holiday season this winter, I would certainly be interested in being a beta tester for you. I am not a programmer, but I understand programming, data sets, file structures, software interfaces, etc. and would love a chance to play around with your concept using my own family data.

I have too many things going for now, but my own family mysteries requires me to pursue this concept further.

You can contact me off-post

N A N C Y at N E D O B A dot O R G
Reply With Quote
Reply

Bookmarks


Currently Active Users Viewing This Thread: 1 (0 members and 1 guests)
 
Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

Forum Jump

Similar Threads
Thread Thread Starter Forum Replies Last Post
Admixture percentages and timeline Mars Family Finder Advanced Topics 5 29th August 2014 01:06 PM
Trace route of mtDNA + Y-DNA pascal the kraut Features Requests & Bug Reports Area 0 23rd October 2011 05:50 AM
Admixture or autosomal tests for percentages? KCat mtDNA - Advanced Topics 50 22nd May 2007 04:47 PM
Curious about your genealogical origins? UA can help trace them 29149 DNA and Genealogy for Beginners 8 29th December 2006 01:15 PM
Y-DNA showing a trace in autosomal scores... NormanGalway DNA and Genealogy for Beginners 0 31st August 2006 01:28 PM


All times are GMT -5. The time now is 07:59 PM.


Family Tree DNA - World Headquarters

1445 North Loop West, Suite 820
Houston, Texas 77008, USA

Phone: (713) 868-1438 | Fax: (832) 201-7147
Copyright 2001-2010 Genealogy by Genetics, Ltd.
Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2018, Jelsoft Enterprises Ltd.