Using the tools at GEDmatch:
When Working with Jewish DNA

 By Kitty Cooper, blogging at blog.kittycooper.com -

slides always at slides.com/kittycooper

This is the home page for GEDmatch

click on top right to sign in or create account

Scroll down that home page and find lots more information

Click the link above to get to the video that explains getting a user id and some of the basics

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 !

My Home page at GEDmatch 

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 bottom of your Dashboard Page 

 

notice the CONTACT US button!

On the top left of your Dashboard Page there is much information to help a new user

 

The reason we are on this site is to use the tools on our DNA test results

 

so first upload your DNA

 

At the bottom right of your dashboard are the tools for family trees stored as GEDCOMs

Next Upload a GEDCOM of your Family Tree 

You can download your family tree as a GEDCOM from Ancestry, MyHeritage, GENI or WIKItree

you can also add your DNA kit to your profile at WIKItree 

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

I recommend uploading a privatized GEDCOM of just your ancestors with no more than 10 generations

GEDCOM + DNA matches

There can be a lot of information on the first page, the individual, in a 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

2 GEDCOMs comparison

The free tools are listed in a panel on the right of the Dashboard

And they are listed with other tools in the side drop in menu (click the hamburger to get it)

If you have just uploaded a kit there are a few things you can do while you wait for it to be ready to use (aka "tokenized")

See these slides of mine for how to use the admix tools: https://slides.com/kittycooper/gedmatch

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. The Eurogenes calculator even has one called Jtest which the creator has disowned!

This result is for a 100% Eastern European Jewish man

You can run the

DNA File Diagnostic Utility 

 

you want to see a

Status: Good

I am often asked about  slimming

 

for the purpose of quick comparisons the heterozygous SNPs are removed because with one of each base, those SNPs match everyone

 

Next check use the "Are your parents related" tool as this can make it harder to figure out new relatives

 

If you are Jewish and your parents have ancestry from the same area, this may show relatedness

 

sample negative result

Example of a positive result for a Jewish man with no known relationship between his parents

The possibilites for 66 from DNA painter

dnapainter.com/tools/sharedcmv4

sample negative result

If you are worried about the health risks from these ROH segments upload your DNA to

The problem with Jewish Autosomal DNA matching is that we are all related!

Lara Diamond is collecting Ashkenazi data and her current report is here: 

https://larasgenealogy.blogspot.com/2022/08/ashkenazic-shared-dna-survey-august.html

Close relationships are within the normal range but at the high end, the average is about 100-200 cM larger than the norm

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)

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

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 which lists all the kits that match the kit number you give it. So an "In common with function"

Note that there are two varieties. The limited version has more information but does not have the full functionality of a paid membership

The original one to many is simpler. It only asks for a kit number.

Then it displays the information below. Click the green A to get the one to one comparison. Click the kit number to see that kit's matches

Kitty's Guidelines for Jewish DNA Matches worth following up on

  • At least one segment > 20 cM
  • Another segment > 10 cM
  • Several more good sized segments
  • Sort by the largest segment

First make your selections on the limited One-To-Many form. the defaults do not include tag groups so check that

I also prefer to raise the minimum cM to at least 12 for Jewish matches or even better 20 cM

note the tips button, click it for more information

The limited 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 that the kit number is colored with its tag group

https://blog.kittycooper.com/2017/04/using-gedmatch-tag-groups/

The limited one-to-many middle section

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, notice that it can be connected to the mitoYDNA web site ....

This old post explains the column headings like Gen

https://blog.kittycooper.com/2016/06/gedmatch-tools-2016/

Every column is sortable, I often sort by largest segment, see

https://blog.kittycooper.com/2015/08/size-matters-for-matching-dna-segments/

Recently I had a close match with a name I did not recognize, 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"

Comparing my Dad and my new Munson cousin

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

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. 

Kitty's Guidelines for Jewish DNA Matches worth following up on

  • At least one segment > 20 cM
  • Another segment > 10 cM
  • Several more good sized segments
  • Sort by the largest segment

Clicking the largest segment on the one to many brings you to this comparison form with the kits filled out

Check this for a more compact display

7 is too small for jewish matching try 10 or 8

One to one with numbers and graphics for jewish second cousins twice removed

One to one with numbers and graphics for jewish second cousins twice removed

One to one with just numbers using 7cM for jewish second cousins twice removed

Relationship Calculator at GEDmatch prediction

This is my late husband compared to the child of his second cousin once removed who donated sperm.

Story is here: 

blog.kittycooper.com/2021/07/a-sperm-donor-is-found-with-dna/

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

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

You can check boxes next to multiple kits and then use the visualize button to use the multikit analysis tools

MULTI-KIT ANALYSIS (Tier 1)

You can do a matching segment search for just the selected kits

Even better is a triangulation for just the selected kits

My Compact Chromosome Browser

The 3D chromosome browser includes multiple matrices, autosomal. X, and number of segments

Can software figure out the family tree from the shared DNA?

AUTO Kinship

The result has to be downloaded

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

https://www.youtube.com/watch?v=AjA59BG_cF4

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

One interesting exercise is to search for matching segments

 

For example when your parents are related you could search for everyone that matches you on that segment

 

or when you have a large single AJ segment match to  a non jewish person

 

this is an upcoming blog post

All my presentation slides are online at slides.com/kittycooper

my blog is at blog.kittycooper.com/

 

Using GEDmatch for JGSNY 2023

By Kitty Cooper

Using GEDmatch for JGSNY 2023

Using the tools at GEDmatch, the Basics for Finding Relatives and more: Presentation by Kitty Cooper http://blog.kittycooper.com

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