Wednesday, January 24, 2018

How to use GEDmatch - Part 2



How to use GEDmatch - Part 2: 
Comparing two family trees, linking ancestors,
 and finding common DNA segments


Before reading this article, it will be very helpful if you have done the following:

  • Download your raw DNA data from your DNA testing company, and upload it to GEDmatch.
  • Download your family tree as a GEDCOM file, and upload it GEDmatch.

You can see step-by-step instructions, including screen images, in Getting started with GEDmatch.

Then see how to do basic comparisons in How to use GEDmatch - Part 1.

Once you've done those two things, you'll be less overwhelmed by the following more advanced procedures for comparing family trees and finding common DNA segments. This is when it really gets great.


The difference between GEDCOM and GEDmatch


We need to be clear about the meaning of two terms because there is a lot of confusion about the terms "GEDCOM" and "GEDmatch."

GEDCOM is an acronym that has been used since the 1980s. GEDCOM stands for GEnealogical Data COMmunication. GEDCOM is a family tree format that can be used to exchange family trees between different websites and genealogical software programs.

GEDmatch is a website where you can compare your DNA results with the results of people who have tested at other DNA testing companies.

Unfortunately, these terms have even been confused on the GEDmatch website.


Attach your GEDCOM to your GEDmatch profile


When you upload a GEDCOM file, GEDmatch assumes that the first person in the tree is the person to whom you are attaching the results. You should verify that the tree is attached correctly.

Get your GEDmatch kit number (or the kit number of another person whose kit you manage), and go to your GEDCOM Resources:


GEDCOM files
Uploaded GEDCOM files


Each GEDCOM is given a number. The GEDCOM numbers are listed in the left column above. Click on the appropriate GEDCOM number to go to the GEDCOM details page.



GEDCOM details



The details page will show the name of the person in the family tree and the kit number linked to this person. If the kit number is attached to someone in the tree other than the person who took the DNA test, unlink the kit number by clicking the blue HERE link. Then go to the correct person in the tree, and enter the kit number in the box. 


Here is a portion of a new family tree once it has been uploaded to GEDmatch and linked:



GEDmatch family tree



A new way to make a match


We are going to see some automated ways to compare family trees, notate matches on your family tree, and let others know about the match. 

Start by comparing your results to everyone in the database. Please note that if you loaded your DNA into GEDmatch within the past 24 hours, you must wait until your kit finishes processing. 

Click One-to-many matches in the Analyze Your Data section.


GEDmatch one-to-many



Enter your GEDmatch kit number on the next screen, and click Submit. Then view your list of matches.

The match list columns were explained in How to Use GEDmatch - Part 1. Below is a partial list of matches with the kit number, name, and email columns removed. Find someone who has uploaded a GEDCOM file, and click "GED" to view the tree.



GEDmatch family tree


You could compare this person's family tree to your family tree, or you can have GEDmatch do it for you. GEDmatch will find all possible common ancestors.

As stated above, there is a lot of confusion about "GEDmatch" and "GEDCOM." Here is an example. In the image below, the "GEDmatch Ref" number should read GEDCOM Reference number, because this is the GEDCOM number, not the GEDmatch Kit number. Copy the "GEDmatch Ref" Number; it is your match's GEDCOM number.


GEDmatch family tree reference number


Go to your home page and click "2 GEDCOMs" in the Genealogy box.


Compare two GEDCOMs


Enter your GEDCOM number and your match's GEDCOM number. Notice that the GEDCOM numbers are all numeric, and the GEDmatch kit numbers begin with a letter.  Be sure you  are entering the all-numeric GEDCOM numbers.


Compare GEDCOMs



You will get a list of possible matching ancestors found in your family tree and your match's family tree. You will also see the following tools:



GEDmatch family tree symbols


You will have to evaluate these matches. Some of these possible matches are not real matches. For example, although these two people have the same names and approximate dates of birth, they have different parents. You would not confirm this as a match.


ancestor compare


When you are sure of a match, click the "Click HERE" link.


GEDmatch confirm match


This will confirm the match. When you have confirmed a match, a new tab will open in your browser with the following message.

Confirmed family tree match


Close the tab to return to your matches. When you have finished, your family tree and your match's tree will have changed. Both trees will have green tree symbols indicating that these people have been found in more than one family tree.


GEDmatch linked tree




Do my match and I share DNA segments?


Once you have compared family trees and found common ancestors, you want to see if you have matching DNA segments. Go to your home screen and use the "One-to-one compare" to compare DNA.


GEDmatch compare DNA



Enter your GEDmatch kit number and your match's kit number on the next page. The GEDmatch kit numbers will each start with a letter. Below, one kit begins with the letter A indicating that this person was tested at Ancestry DNA. The other kit begins with a T and was tested at Family Tree DNA.


one-to-one DNA comparison


Click Graphics and Positions, then click Submit.

Here is an example of one of the matching DNA segments.


GEDmatch chromosome browser


If you click "Position Only" instead of "Graphics and Positions" in the Comparison Entry Form, you will get a nice table that you can use when you transfer these segments to a database or to a tool like DNA Painter.


matching DNA segments



To see what you can do with these segments, please see Using DNA Painter to reconstruct ancestral DNA.


Tree symbols on your family tree


What if you see the family tree symbol in your own family tree? You can find out who created this link, and see if you have any matching DNA segments.   

I found these links on one of my family trees, but I did not create them. Click the green tree symbol.


GEDmatch linked family tree


You will be taken to the ancestor in your family tree. At the bottom of the screen you will see "Other GEDCOMs that include this individual." This section does not list all GEDCOMs that contain your ancestor; it only lists GEDCOMs that somebody has linked.



GEDmatch ancestor



Click the GEDCOM number. Now you will see your ancestor as he appears in your match's family tree. A link to your tree will appear at the bottom.


GEDmatch ancestor

 
Both people can now see that this ancestor appears in another person's tree. If more than one person linked these ancestors, the bottom of the screen would appear like this:


Linked GEDCOMs



Someone linked the ancestors, but do we share DNA?


We have found a common ancestor, and we want to see if we have any matching DNA segments. There is no link to this person's DNA kit on his family tree page; there is only a link to his GEDCOM. But we can use his GEDCOM number to find his kit number. Copy the "GEDmatch Ref" number. 



GEDCOM number


Go to your home page, and click User Lookup in the Learn More section. You can use this field to look up someone by GEDmatch kit number, GEDCOM number, or email address.



GEDmatch user lookup


You copied the GEDmatch Ref number which is actually his GEDCOM number. Enter the "GEDmatch Ref" into the "GEDCOM (genealogy) ID number" field. Then click Display Results.



GEDmatch User search



You will see this person's GEDCOM number, the name of the person who took the DNA test, email address, GEDmatch Kit number, and the name and email addresss of the person managing the kit. Copy the Kit number that appears directly above your match's name. Kit numbers are used for DNA matching.



GEDmatch user


Now you can do a One-to-one comparison to find matching DNA segments. Enter your kit number and your match's kit number.



GEDmatch one-to-one


Here are the matching DNA segments!



matching DNA segments



What is really nice about GEDmatch is that when we all work cooperatively finding and linking common ancestors, we will more easily prove the relationships with DNA.

Once you know your match's kit number and GEDCOM number you can do complete family tree and DNA comparisons to find DNA that you inherited from your common ancestors.



What's next?

.
Verify that your GEDCOM is correctly linked to your GEDmatch kit.

Practice the comparison tools.  It will be a little frustrating, because you will have to switch screens multiple times. But the results are worth it. The matching results are why you uploaded to GEDmatch in the first place!

Learn about a great tool for displaying your DNA matches. You'll love this one! See Using DNA Painter to reconstruct ancestral DNA.

How to use GEDmatch - Part 3 will be coming soon.

Monday, January 22, 2018

How to use GEDmatch - Part 1


What is GEDmatch?


GEDmatch.com is a volunteer-run website for people who have already tested their autosomal DNA at DNA testing companies such as AncestryDNA, 23andMe, Family Tree DNA (Family Finder test only), and MyHeritage DNA. At GEDmatch you can compare your DNA results with the results of people who tested at other DNA testing companies.

GEDmatch has wonderful tools to enable you to contact your DNA matches, compare family trees, and see matching DNA segments.


Getting Started with GEDmatch


If you don't have an account, go to GEDmatch.com and create one.



GEDmatch login


To get the most from GEDmatch, you will need to load two things:
  • Your raw DNA data from your DNA testing company
  • Your family tree

To see how to upload these two items to GEDmatch see Getting started with GEDmatch

Now log onto your account, and let's examine how to make matches.



One-to-Many Matches


Click the One-to-many matches link in the Analyze Your Data section.



GEDmatch One-to-many



On the next screen, enter your kit number.  If you administer several kits, you can select the kit number from the drop-down menu.


GEDmatch kits


Click Display Results at the bottom of the screen.

Your list of matches will appear on the next page.  It will look overwhelming at first, but don't give up! Let's look at the table headings.


GEDmatch headings

  • Kit number is the number assigned by GEDmatch. Each kit begins with a letter that indicates the testing company. For example: A is for Ancestry DNA; H is for MyHeritage; M is for 23andMe; T is for Family Tree DNA's Family Finder.
  • Type is the type of testing chip used by the DNA testing company.
  • Use the List column to display a list of people who share DNA with one of your matches.
  • Use the Select column to compare two or more kits.
  • Sex is for the sex of the person taking the test.
  • GED/WikiTree contains a link to your match's family tree. GED indicates that it was uploaded from a GEDCOM file. Wiki is a link to WikiTree.
  • The haplogroup columns are not very useful since they are for Mitochondrial DNA and Y-DNA. GEDmatch only compares autosomal DNA. However, if you are searching for your direct paternal or maternal line, this column can indicate if your match is within the same ancestral haplogroup.
  • The Autosomal Details column is a column you will use frequently. You will click a blue A link to see a comparison of your DNA to your match's DNA.
  • The Autosomal Total cM indicates the total amount of shared DNA between you and your match. It is measured in centiMorgans. Largest cM is the amount of DNA in your largest shared DNA segment.
  • Gen is the estimated number of generations to your shared ancestor.  This is only an estimate and will often not be accurate.
  • The X-DNA columns are similar to the autosomal DNA columns. Click the X in the Details column if you want to compare shared DNA on your X chromosome. Please note that X-DNA is not the same as mitochondrial DNA. They have very different inheritance patterns. The difference will be shown later in this article.
  • The last two columns are very important. They contain the name or alias of your match and the email address. This is especially useful when your DNA company does not provide email addresses.

You can sort your matches by any of these columns. For example, if you want to sort your matches by the size of the largest X-chromosome segment, click one of the blue arrows in the X-DNA largest cM column. If you are sending an email to someone and you want to see multiple kits managed by this person, click the blue arrow under the Email column.

Find the common ancestor


Here is a partial list of matches from the One-to-many comparison. The columns for Kit number, name, and email have been removed. You want to see if you can find a common ancestor between you and your match.  Often you will find a common ancestral couple from whom you both descend. See if your match has a family tree. Click the link in the GED/WikiTree column.



GEDmatch family tree


If there is no link to a family tree, you may wish to contact your match to see if he/she has an online family tree. 

There will not be a GED or Wiki link next to your own kit unless you loaded a family tree. If you haven't, please fix it! See Getting started with GEDmatch.



Comparing family trees


I have contacted one of my matches who did not yet load a family tree to her GEDmatch account. Her name is Debra, and we compared family trees at Ancestry.com. Below is my family tree. 


pedigree chart

  
Here is Debra's family tree.



family tree


Our common ancestors are Willis Collinsworth and Laura Burleson. Debra probably inherited a lot more DNA than I did from Willis and Laura because they are her great-grandparents, and they are my 3rd-great grandparents.


Comparing DNA


Now we get to the best part of GEDmatch--viewing the DNA you have in common.

Click the A in the Autosomal Details column to compare DNA.


 autosomal DNA match


When you click the blue A you will be doing a one-to-one comparison. 

The two kit numbers (yours and your match's) will be automatically entered into the entry form. Click Graphics and Positions to view a complete match. Click Submit at the bottom of the form.


one-to-one comparison



You will see the chromosome browser on the next page.  When you click "Graphics and Positions" you see a graphical representation of your chromosomes. If there are any matches they will be highlighted with the following colors. The blue Matching segment size will change based on the settings you set in the Comparison Entry Form; 7 centiMorgans is the default size.


GEDmatch color key


You can change the segment sizes in the chromosome browser by entering a different value in these sections:

GEDmatch segment defualts


For example, if you change the Minimum segment cM size from 7 to 10, your key will appear as follows.


GEDmatch color key


Comparing my DNA to Laura's, we see in the chromosome browser that our only common DNA was found on Chromosome 5. The blue bar indicates that the segment size is greater than 7 centiMorgans. The yellow tells me that this is a "Half Match" meaning that it came from only one of my parents.  The Position table above Chromosome 5 tells the exact chromosome position and size of the match.


GEDmatch chromosome browser


Since I know the common ancestral couple, I can begin to prove that the segment on chromosome 5 was inherited from either Willis or Laura. A DNA match to one person is not enough to prove that this DNA segment was inherited from Willis or Laura.  It could have come from another common ancestor that we have not yet identified. I need to find other descendants of Willis and Laura who share the same DNA segment. There are many tools to do this. One great tool is DNA Painter. See the link at the bottom of this article.

We will examine some of the other tools in future articles.



Mitochondrial DNA (mtDNA) and X-chromosome DNA (X-DNA)


As mentioned earlier, the inheritance patterns of mitochondrial DNA and X-DNA are different.  Mitochondrial DNA is found outside the nucleus of the cell.  The X-chromosome is found inside the nucleus of the cell.

Mitochondrial DNA inheritance

Mitochondrial DNA is inherited from your strictly maternal line (your mother's mother's mother . . .). Both males and females inherit their mother's mitochondrial DNA, but only females can pass it to their children. Mitochondrial inheritance is shown below in red.


Y-DNA and mtDNA inheritance
Inheritance of Y-DNA [blue] and Mitochondrial DNA [red]


X-DNA inheritance for males


Males have one X chromosome and one Y chromosome. 

Below is a fan chart [a version of a family tree] for a male. The man's name would go in the circle at the bottom of this family tree. His father's name would go in the first space on the left directly above the circle. His mother is the first space on the right directly above the circle. A man cannot inherit X-DNA from any ancestors on his father's side of the family. The male and female ancestors from whom he could have inherited X-chromosome DNA are highlighted in blue for males and pink for females. Here is the pattern of X chromosome inheritance for a male. 


X-DNA inheritance
X-DNA inheritance for males



 X-DNA inheritance for females

A female inherits two X chromosomes--one from the mother and one from the father. In the pedigree chart below, the female's name goes in the pink circle at the bottom. Her ancestors are displayed above. Here are the possible ancestors from whom a female could have inherited X-chromosome DNA.


X-DNA inheritance
X-DNA inheritance for females

 
My match and I share the common ancestors Willis Collinsworth and Laura Burleson. Here is a fan chart of my ancestors pointing the common ancestral couple. I could have inherited X-DNA from either of them.


Fan chart


Again, we see the same family tree shown in pedigree view.

Family Tree at Ancestry.com


Here is the family tree for my match, Debra. Compare these ancestors to the above fan chart for X-DNA inheritance for females. Debra also could have inherited X-chromosome DNA from either Willis or Laura.


Ancestry family tree



Comparing X-DNA segments in GEDmatch


In addition to the match on chromosome 5, Debra and I have a match on the X chromosome. Debra's kit is the third kit in the image below. Click the blue X link to see the X-DNA match.


GEDmatch headings
GEDmatch X-DNA



In the X-DNA Comparison Entry Form, click on Graphics and Positions, then click Submit.


GEDmatch X-DNA comparison


Using the default settings I see the following:


X-DNA chromosome browser


In the One-to-many match results, it showed that Debra and I share a total of 72 centiMorgans on the X chromosome. 

X-DNA segment size


Because I used the default settings for the one-to-one comparison, the X chromosome browser is showing the largest segment, but no other segments.

Although the X-DNA Comparison Entry Form allows me to change the default values, it does not state what the default values are. However, they are the same as the defaults for the autosomal DNA comparison.

The default value for SNP count minimum threshold is 500, and the default for Minimum segment cM size is 7. I will see a difference in the results in the chromosome browser if I experiment with the settings:

GEDmatch default settings


Here are the new X-DNA chromosome browser results: 


GEDmatch X-DNA comparison


Knowing that Debra and I share segments on the X-chromosome is more evidence that we share Willis Collinsworth and Laura Burleson as our common ancestors.


What's next?


Experiment with your GEDmatch account. 
  • See your list of DNA matches by clicking the One-to-many matches link.
  • Use the GED/Wiki column to see family trees and find common ancestors. If you don't see a family tree link, contact your match using the email address in the Email column of your match list.
  • Try the One-to-one autosomal comparison by using the blue A link.
  • Try the One-to-one X-DNA comparison by clicking the blue X link.

After that, see the following: