My slides are always available at https://slides.com/kittycooper
A Beginner's Guide to GEDmatch
By Kitty Munson Cooper
Blogging at blog.kittycooper.com
This is what you see when you go to GEDmatch.com - the front page or landing page for GEDmatch
Go to the GEDmatch education page for many videos, no log in needed gedmatch.com/education/
CIick the link in your handout for a video on how to register for GEDmatch and upload your DNA or copy the link below
GEDmatch was founded to let you compare GEDCOMs and autosomal DNA results from different companies with powerful analysis tools
A problem is that the various DNA testing companies test different SNP sets which are not the same although there is much overlapping
So GEDmatch developed a special template for comparing them !
Your dashboard (aka home) page has much help for new users plus messages about what's new on GEDmatch
When you log in your information and uploaded resources are listed on the left side of the page below the day's messages and the welcome
We call this the Dashboard Page
The very bottom of your Dashboard Page
notice the CONTACT US button!
The top right of your Dashboard Page
has information items
notice the Support Request link!
How to Use GEDmatch brings you to this welcome page
The free tools are listed in a panel on the right of the Dashboard
And they are listed with other tools in the left menu you get when you click on the hamburger. Wide screens get a top menu instead
Clicking the hamburger at the top left slides in this menu, click the X to get rid of it
In order to use the tools at GEDmatch you need to have uploaded a DNA kit.
Even if you have been sent a kit number, the tools won't work
If you have just uploaded a kit, there are a few things you can do while you wait ( a day or two) for it to be ready to use (made into the GEDmatch template aka "tokenized")
See these slides of mine for how to use the admix tools: slides.com/kittycooper/gedmatch
Reminder, the slides for all my past presentations are at
You can play with the admixture tools, many have not been updated in years but they are still fun and different from your testing company
I am often asked about slimming
for the purpose of quick comparisons the heterozygous SNPs are removed because with one of each base, those will match every base pair
Next check use the "Are your parents related" tool as this can make it harder to figure out new relatives
Unless you are from an endogamous population or know your parents are cousins this will likely be negative
sample negative result
sample negative result
people from endogamous populations often find that their parents are distantly related
At the bottom right of your dashboard are the tools for family trees stored as GEDCOMs
Please create, upload or import a GEDCOM of your Family Tree
You can download your family tree as a GEDCOM from Ancestry, MyHeritage, GENI, WIKItree or any genealogy program
you can also add your DNA kit to your profile at WIKItree
What is a GEDCOM -https://en.wikipedia.org/wiki/GEDCOM
I recommend uploading a privatized GEDCOM with about 10 generations of ancestors for your kit
Since a GEDCOM is a text file, you can edit it in a plain text editor like the notepad on a PC
I recommend changing the first names of anyone living to just LIVING
and removing birth month and day leaving the birth year
Another great free tool lets you look at the GEDcoms of your DNA matches who have uploaded them
GEDCOM + DNA matches
Click the GEDcom id to see that tree
When you click that id, the first page shows just an individual.
This has some useful information,
especially in your own gedcom
But typically we just click to see the pedigree
Top half of my Aunt's pedigree, the clickable little tree shows where a match to another GEDCOM has been confirmed
Have a look at the GEDCOM comparison tool
2 GEDCOMs comparison
The next thing to do is set up your tag groups
You need to know the kit numbers of your known relatives (easier once you can do a one to many)
Your profile is on the left above your resoures
The next page has a set of tabbed headings; click on Tag Group Management
I recommend setting up a group for each great grandparent line using the same colors you used at Ancestry or on your Leeds Chart
Also perhaps a group for close family and for localities see
https://blog.kittycooper.com/2017/03/gedmatch-tag-groups-plus-new-one-to-many/
Click on the green button Display/Edit tag group to get to this page
Once you have created a tag group. add the kit numbers of your known relatives at GEDmatch via the Manually Add Kits
The page with the form to Manually Add Kits
Once you have a GEDCOM uploaded and tag groups set up, it is time to use the most important tool for finding relatives: the One-To-Many
Counter intuitively the "limited" version has more functionality than the original
The original one-to-many shows the kits that match the kit number you give it with the overlap indicating how many SNPs are in the comparison, red means too few, and it shades down from there
Notice the concealment of the email address, clicking on that takes you to the user lookup for just that kit
Example of a user lookup from the original one-to-many
First make your selections on the the One-To-Many form. the defaults do not include tag groups so check the One
I also prefer to raise the minimum cM to at least 10 and for endogamous people to 20 cM
Example of the limited one-to-many,
every column is sortable
Notice that the kit number is colored with its tag group
https://blog.kittycooper.com/2017/04/using-gedmatch-tag-groups/
If the kit is connected to a GEDCOM or to a tree at WIKItree that shows here
The haplogroup information is entered by the user, note that it can be connected to the mitoYDNA web site ....
This old post explains the column headings like Gen
Every column is sortable, I often sort by largest segment, also any entry that is blue is clickable see
blog.kittycooper.com/2015/08/size-matters-for-matching-dna-segments/
The haplogroup information is entered by the user, note that it can be connected to the mitoYDNA web site ....
Recently I had a close match with a name I did not recognize and no tree, so I clicked on her kit number to look at her one to many
I could tell immediately from the tag group colors of her matches that she was a Munson
If tag groups don't solve where a match is related try
the ICW function:
"People who match
one or both kits"
The match button on the one to many list will bring you to this page with the kit numbers filled in
Comparing my Dad and my new Munson cousin
Sometimes when they have no tree it is because they do not know it
My new 3rd cousin was looking to find out who her dad was. Happily I was able to figure it out for her.
Some of the FREE tools that I find invaluable are highlighted
Checking my new cousin in the relationship probability tool by entering the shared cM
To summarize this first part
Uploading a family tree (GEDCOM) will help you figure out DNA relatives
Setting up tag groups will also help figure out new family members
You need to setup a login and to upload a DNA kit to make use of the GEDmatch tools
The various one-to-many functions are how you find your DNA relatives
SEGMENT DATA
A matching segment of DNA is where a long run of SNPs are the same in two different kits. The problem is that the testing process cannot tell which side they are from. Thus the match can even be from a mix of the two sides, maternal and paternal.
These links are in your handout as are most in this talk
https://segmentology.org/2015/05/07/what-is-a-segment/
https://blog.kittycooper.com/2014/10/when-is-a-dna-segment-match-a-real-match-ibd-or-ibs-or-ibc/
To look at what segments in your genome are a match to a DNA relative click the number under largest segment
That will take you to the form for the one to one comparison with the kit numbers filled in
Note that clicking on the kit number takes you to the form for listing the one-to-many for that person
Clicking the largest segment on the one to many brings you to this comparison form with the kits filled out
One or two items might be changed for the display, else the defaults are fine
One to one without the graphics, position only, min of 10 cM
My double third AJ cousin
One to one with numbers and graphics (partial page)
My double third AJ cousin
One to one just graphics with my double third AJ cousin at min = 7cM
Full siblings always have some fully identical regions (FIRs) - where both strands of DNA got the same SNPs from their parents - those are the green bars
this is the graphic only, one-to-one, for my brother and myself
FIR only version of my comparison of my brother and my Ancestry kits
One to one on the X chromosome with my double third AJ cousin
Example of an X one to one from clicking on largest X segment
New exciting tools typically come to Tier 1
The first thing to do is make a combined kit if you have tested at multiple companies
If you have tested at more than one company, since they may have tested some different SNPs, best to upload both and combine them into a super kit (then mark the base kits research) see
https://blog.kittycooper.com/2019/04/make-a-combined-dna-kit-for-yourself/
Visual comparison of my 23andme kit to my Ancestry kit
Tier 1 One to Many full version with one Tag Group
You can check boxes next to multiple kits and then use the visualize button to use the multikit analysis tools
Clicking on the total shared brings up the relationship estimate, while the largest segment still goes to the one to one
MULTI-KIT ANALYSIS (Tier 1)
when you click multiple check boxes on your one-to-many then click the visualize button it takes you to this page of choices
You can do a matching segment search for just the selected kits
Alternately you can do a triangulation for just the selected kits
My Compact Chromosome Browser
The 3D chromosome browser includes multiple matrices, autosomal. X, and number of segments
FInd common ancestors with your DNA matches
CLUSTERING
Set the parameters for clustering, raising the low end will give clearer boxes
The result has to be downloaded
Can software figure out the family tree from the shared DNA?
AUTO Kinship
After you download it and unzip it click on the folder Autokinship then on the HTML file autokinship to see a long page in your browser: first the clusters
My auto kinship clusters
one endogamous population grandparent, and another missing from the testing community
Since so many of my MUNSON cousins are tested ... what would autokinship came up with for that cluster 2 green box?
Lauritz + Josephine Monsen
Inga
Lawrence
Alfred
Christian
Pretty accurate. I have identified which child of my great great grandparents each match is descended from. Only the last one is not, he is actually descended from a sister of Josephine's
?
A closer look at my cousins with the one generational correction
?
Next is a matrix of how many cM they each share with each other
And finally there is a list of shared segments that met your criteria
Tim Janzen did a great Rootstech talk about these new features at
Shall we look at the auto tree for my endogamous cluster?
Here are the few trees created for cluster1 - the problem is not enough kits have linked trees on GEDmatch
Gugenheimer and Thannhauser are known ancestral lines, not Shadur
Phasing
- If you have at least one parent tested then you can separate what you got from each parent
- If the maternal or paternal phase can be determined the values will be assigned else the original unphased values will be kept
LAZARUS lets you create a kit for comparisons for a person who cannot be tested from their close relatives
There are many more fun Tier 1 tools you might try
