Raw Data Tools

[daveungar]

Are there 3rd-party tools available for analyzing the Family Finder Raw Data? There are several types of analysis I'd like to perform that the built-in Matches and Chromosome Browser can't do well.

As an example, I have tested several relatives and often get questions from matches asking to correlate information between relatives. One tool that would be nice would take several sets of raw data and show all the correlations of a certain length, etc.

Any suggestions would be appreciated as I'm relatively new to genetic genealogy.

[vinnie]

You can do quite a bit at www.gedmatch.com

[mkdexter]

lots here too:

http://www.23andyou.com/3rdparty

note the URL says "...you" not "...me"

[thetick]

If you are computer savvy, I made a list of DIY Calculators. I originally posted it on another forum which I'm not allowed to link at the forum so I'll post the contents below:

1 )DIYDodecad 2.1 - note deprecated version 2.0 and 1.0 that have issues with recent data

http://dodecad.blogspot.com/2011/09/do-it-yourself-dodecad-v-21.html

also
http://www.gedmatch.com - Admixture Utility

2) K7b Dodecad

http://dodecad.blogspot.com/2012/01/k12b-and-k7b-calculators.html

3) K12b Dodecad

http://dodecad.blogspot.com/2012/01/k12b-and-k7b-calculators.html

4) K12a Dodecad

http://dienekes.blogspot.com/2011/12/first-analysis-of-metspalu-et-al-2011.html

5) eurasia7 Dodecad

http://dodecad.blogspot.com/2011/10/eurasia7-calculator.html

6) world9 Dodecad - has Amerindian!

http://dodecad.blogspot.com/2011/12/world9-calculator.html

7) bat (Balkans-Anatolia-Turkic) Dodecad

http://dodecad.blogspot.com/2011/09/bat-calculator-balkans-anatolia-turkic.html

8) africa9 Dodecad

http://dodecad.blogspot.com/2011/09/africa9-calculator.html

9) weac (West Eurasian cline) Dodecad

http://dodecad.blogspot.com/2011/09/weac-calculator.html

10) euro7 Dodecad

http://dodecad.blogspot.com/2011/09/euro7-calculator.html

11) MDLP (Magnus Ducatus Lituaniae Project)

http://magnusducatus.blogspot.com/2011/08/i-have-modified-diydodecad-calculator.html

12) Eurogenes test (DIY West Eurasia)
-- Bad link -- appears gone.

13) Gedmatch Eurogenes K12b Admixture

http://ww2.gedmatch.com:8007/autosomal/ap_mix1ww_euro.php

14) Magnus Ducatus Lituaniae Project DIYDodecad (K=5...K=15)

http://www.forumbiodiversity.com/sho...postcount=1604

Note K=13 appears to have a bogus Altaic component and some have been added to gedmatch

15) DIY HarappaWorld

http://www.harappadna.org/2012/05/diy-harappaworld/

[Elena Govor]

I am not computer savvy and would appreciate suggestion about a program for the particular type of analysis.

I am managing account of my husband and his 2nd cousin. They have a number of common matches (quite numerous as they both are Jewish). I am trying to find 'genuine' matches among these matches, i.e. those who will match my husband and his cousin on the same section of chromosome.

Currently the only way I know to do this is very time consuming. I open Chromosome browser from my husband's page and open his match common with the cousin. Then I log out, open new internet window with from his cousin's account and open in his chromosome browser the same common match. After that I can visually compare if the common match matches my husband and his cousin on the same sections of chromosome.

It would be great to find a way for such comparisons using excel table that we can download from chromosome browser (with data about chromosome, start and end of matching blocks). I envisage a program where I could load excel table of my husband's matches with several people and then a similar table of his cousin's matches with the same people and to get result indicating matching blocks of chromosomes.

I think the more relatives we test the more useful such comparative tool would be. I hope that great specialists that we have here will be able to help!

[1_mke]

Elena,
One suggestion I have is to use two different browsers so you don't have to constantly login/logout. I use Chrome and IE. This keeps my credentials seperate between the two browsers.

[Colin]

I copy and paste the data from Chromosome Browser to a spreadsheet, for the three kits i manage, then see how and where they overlap

[JSW]

In common with

Here is a procedure for using gedmatch.com
It has the advantage of picking up matches to those 23andMe people in
the database but will miss those FTDNA kits not in gedmatch.com

I suggest using 3 browser windows but you can do it with one
After uploading both sets of raw data and waiting the 24 hours for batch processing
In window A use the compare two IDs tool to get the segments that are
in common between you two cousins two.
In window B use the compare a segment tool against person 1
In window C use the compare a segment tool against person 2

Matches in common are just that and they are close to being
phased matches as you use both person 1 and 2
Matches not in common will be on the other "phase" of that DNA kit.

Go through this segment by segment to as small a segment as you wish
I would not go below 3.5 cM as that will be noise

As a time saver when going from one segment to the next
I edit the URL line rather than go back to the menu entry for the
segment search. I just change the chr, start and end numbers
I do not bother with exact start and end position number
I just go to the nearest million. I go up to the next million on the end
and down to the million on the start. Thus it is only 2 or 3 digits to enter

[Elena Govor]

In common with

Thank you all for the responses.

The only problem in my case is the huge number of 'in common with'. They number 200-300 matches between my husband and each of his 2nd cousins. My methodical check of all common matches between him and one of these cousins showed that only about 20 out of 200 matches share the same sections of chromosomes (above 3 cM). To do this analysis took me ages and I just thought that if such sophisticated ways of analysis are being introduced on the gedmatch, perhaps some computer wizard will be able to invent a tool which will optimize such search for 'real' matches between all matches of two persons.

[lanajane]

Recently, there was discussion about exporting raw data from the FTDNA Chromosome Browser into GEDMATCH and using their Chromosome Browser, so you can see EVERYONE from your matches and on which chromosomes they match you. I am getting ready to do this, but I wanted to see if the method I'm going to use is the most efficient. I will take 5 matches at a time (since that's the limit), put them on the FTDNA browser, export all of that data into Excel. Once I have my humongous spreadsheet, I'll then upload that to GEDMATCH.

Is this right? That spreadsheet is going to be a monstrosity!!

[prairielad]

Recently, there was discussion about exporting raw data from the FTDNA Chromosome Browser into GEDMATCH and using their Chromosome Browser, so you can see EVERYONE from your matches and on which chromosomes they match you. I am getting ready to do this, but I wanted to see if the method I'm going to use is the most efficient. I will take 5 matches at a time (since that's the limit), put them on the FTDNA browser, export all of that data into Excel. Once I have my humongous spreadsheet, I'll then upload that to GEDMATCH.

Is this right? That spreadsheet is going to be a monstrosity!!

you can make one excel file, but Gedmatch gives you the optional of adding additional files once one is uploaded.

For example if you have 100 matches with FF you can save 20 excel files(5 matches to each file) then upload each one after another at Gedmatch.

At Gedmatch at one point it will ask you if you have another file to upload, just follow the prompts.

I found this method easier then trying to combine each file into one then uploading.

[boi568]

What I did (although I do have that monstrously large spreadsheet) was to download the FTDNA raw data in one shot to my computer, then upload that file, unzipped, into Gedmatch. Seems much easier.

[Colin]

isnt there a facility to just import the matches to gedcom direct?

[Colin]

Upload your FTDNA FF match results file
For use with Triangulation utility

As part of your Family Finder results, FTDNA provides a downloadable file that contains the names and results for all your matches. By loading that information into the GEDmatch.Com database, you can get a list of people who have the same matches as you. This provides the basic information you need to 'triangulate' on a common ancestor.

INSTRUCTIONS:
1. Log in to your FTDNA account.
2. Under the 'Family Finder' tab, click on 'matches'.
3. Make sure the 'Relations' filter is set to 'Show All Matches'.
etc.

but not sure if that includes the dna from the chromosome browser