Tag Archive | GEDmatch

When the DNA says your parents are related

Jul25

One of the first things I do when helping someone with their DNA results is to check if their parents are related. This can explain unusual patterns of matches, for example, all seemingly from one side.

GEDmatch.com has a nice tool called “Are Your Parents Related” (AYPR) in the”Analyze Your Data” blue panel (middle right of page) which looks for places in the specified kit where the DNA is identical on both chromosome pairs, maternal and paternal. This happens when you inherit the same segment of DNA from each parent because they are related. We call this a homozygous run which is a fancy way of saying a stretch of identical DNA on both sides.

CeCe Moore specializes in helping people who make this discovery. Click here for the informational brochure she helped Brianne Kirkpatrick, genetic counselor, create. It includes where to get emotional support.

My goal is to help you figure out what the DNA means yourself. Can you deduce what the relationship of those parents is? Well a very simple rule of thumb is to multiply the shared DNA from AYPR tool by four and look up that new total at the DNA painter calculator for the possibilities. Then do further family DNA testing to confirm.

Why does this work? Let’s look at the numbers. Suppose your parents share 25% of their DNA. They will pass about half of that to you, so 12.5%. However only about half of that will be the same DNA so it will show up as about 6.25% on the AYPR tool.

Look at the image. The total is 215.3 when you multiply by 4 you get 861.2. You might look that up before you read on …

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Getting Started with GEDmatch

Jun23

UPDATE 18-AUG-2019: Although many of the concepts in this post are good to know and the ethnicity calculators are not changed. The GEDMATCH site has had a facelist and hes been replaced by what was previously called the GENESIS site. So better to read the following posts:

 

If you and a relative have tested your DNA at different companies, you can compare your results at a free third party site – GEDmatch.com – which also has many additional, useful tools for analyzing your DNA and looking at match lists. Learning to use those tools may take some time as they are not intuitive, so I am writing this post to help a friend, Barbara, start to use them.

The GEDmatch site can be intimidating for the less computer savvy. Like most any place on the web, you have to register by creating a username (your email) and password . Click here for more details on registering in my GEDmatch Basics presentation starting on slide 2. Please do not be put off by the extensive new Terms of Service you have to agree to. GEDmatch has to meet the current EU requirements plus they need to warn you that your DNA could be used to identify a victim or catch a criminal among your relatives.

Once you have a username and password and log in, you are presented with a home page which, again, is not very user friendly. The first task, which we already did Barbara, is to upload your DNA test data. Start with this slide https://slides.com/kittycooper/gedmatch-10-13#/9 for the details of how to upload and manage your DNA results, known as kits, to GEDmatch.

The image to the left shows the big blue box, called “Analyze Your Data,” which you can find on the right side of your GEDmatch home page. I have put a red box line around the functions that I find the most useful. One of the first things I do for a newly uploaded kit is check if the parents are related (yours were not Barbara, nor Martin’s).

Once your kit is uploaded, it still has to be “tokenized” which you can think of as being put into chunks for the template they use for comparisons; this can take 24 hours or so. While you wait to be able to use your kit to look for matches, you can play with the ethnicity tools. Please remember that figuring out the groups you descend from is a science still in its infancy and far from accurate yet, other than in the broad strokes.

Start with Admixture (heritage). For most Europeans, the Eurogenes calculator is best and the default K13 is fine, but for those of us with mainly Northern European ancestors, K12 is better. I have a whole presentation on just these calculators at https://slides.com/kittycooper/gedmatch#/

Although its creator has disavowed the Eurogenes Jtest calculator for listing your Jewish percentage (click here for his article), I find that if you add up all the obvious ethnicities: Ashkenazi, Western_Med, Eastern_Med, West_Asian, and Middle_Eastern, it is not that far off. The Jtest image above is from Martin, the only person I have ever seen AncestryDNA call 100% European Jewish; most of my jewish friends come out between 87% and 98% there.

Click here for the creator, Davidski’s Eurogenes blog posts on Gedmatch. Two important take-aways for me are that his ancestral clusters are much further back than the main companies and any ethnicity of 1% or smaller is likely noise.

Once your kit has tokenized, you can start using the most important tool, the One-to-many compare function which will compare your kit to all the kits in the database and then list your closest DNA relatives.

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GENESIS from GEDmatch: the new chip

Dec15

Technology never stands still. The latest change affecting all of us who love using DNA for genealogy is a new chip from Illumina. The past six or so years of autosomal DNA testing have shown that the current chip is great for testers with European ancestry, but does not have enough SNP coverage to figure out the details of the ethnic make up for people from other parts of the world. Many more and different SNPs are tested in this new GSA chip.

All the 23andMe tests done since this past July use that chip, as does Living DNA (highly recommended if you have British ancestry since it does local regional breakdowns). I imagine eventually the others will follow along. The bad news is that there is not that much overlap between this chip and the previous ones, which affects cousin matching.

Debbie Kennet wrote a blog post describing the new chip at https://cruwys.blogspot.com/2017/08/23andme-launch-new-v5-chip-and-revise.html

Because the SNPs are so different the DNA results from these kits cannot be uploaded to GEDmatch, however our friends there have built another site to handle these new kits called GENESIS. They have come up with a whole new algorithm for relative matching that works with lower SNP counts.

At the recent i4GG.org conference (videos coming in February), I gave a presentation on what’s new at GEDmatch, the second part of it went into much detail about GENESIS, starting with this slide:
http://slides.com/kittycooper/gedmatch-10-13-23#/38

The functions available at GEDmatch are being gradually implemented at GENESIS. Most of the key ones are there now. Plus there is some new functionality. One major addition is the showing of the number of SNPs actually overlapping between kits. Very important to know since the overlaps can be as small as 108,000 SNPs or as large as 580.000.
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Family Trees are now linked to from the GEDmatch Tier 1 One-to-Many

Mar24

The new Tier 1 one-to-many at GEDmatch includes a link to your match’s family tree when that is available. Clicking the word GED next to that kit’s email address takes you to the tree your match has uploaded to GEDmatch. The word WIKI links to the compact tree view at WikiTree.

GEDmatch GEDCOM link

Clicking on the GED for a match takes you to the profile of the individual in the linked tree at GEDmatch.

Here is what you would see if you clicked on the GED next to my Dad’s name. Note the words “GEDmatch Ref: “ followed by a long number. That number is the id of this GEDCOM which you can use to compare to your own GEDCOM in the “2 GEDCOMs “ function on your home page.

Of course, I immediately click on the pedigree button in the little menu at the top of this individual page and then look through the pedigree on the next page for familiar names and places. Here is what the top half of my Dad’s tree looks like at GEDmatch. Note the default number of generations shown is 5. You can change that to a larger number (I often go to 8) and then click submit to see more generations.

WIKI link

Clicking on WIKI next to a match in the Tier 1 One-to-Many listing takes you to that match’s compact pedigree at the collaborative world tree WikiTree. This is automated and the connection to Wikitree happens because a member of that site has added a GEDmatch kit number to a profile there. Here is the top piece of what you see when you click on my WIKI.

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GEDmatch Tag Groups plus new One to Many

Mar20

Being able to group my cousins from different lines into colored “tag groups” on the GEDmatch site is a wonderful new feature. It makes it easy to quickly see which line a new cousin fits into because the new Tier 1 one-to-many display uses those colors to highlight the kits belonging to a group. See the image below for a colorful example of my own one-to-many.

Tag Groups

Tag groups are for everyone, not just tier one members,. They can also be used to select what to look at in the “Multiple kit Analysis” function. However they are not yet included in any of the other functions, like the people who match both kits, triangulation or matching segments and of course not the regular one-to-many.

UPDATE 26 Jan 2021: Both Beta One-to-Many Tools include tag groups but you have to check the box for them, either one or all.

Tag Group Selection in beta One-To_many, my purple outline

Here is a quick example of how a new close cousin can be visually assigned to a line when you use the tier 1 one-to-many on their kit. My tag groups use yellow for close family, aqua for paternal first cousins, shades of blue for my Etne lines, green for my Munson line, and purple for my Wold line. Which line is this cousin on?

Right, she is a Munson.

Other New Features

I love that the newest pages at the GEDmatch site include a top menu. and use tabs to make for a more compact display

Also the new Tier 1 version of the one-to-many is outstanding. In addition to showing those colored tag groups. it has search boxes at the top of every column for just that column. The form to invoke the one-to-many is gone, instead the selection is neatly across the top so you can change it dynamically. The long details that used to be at the top of the page now only show up as a pop-up window if you click the tip button.

Yesterday I did a presentation on all of this, click here for the slides which show many of the details of these new features.

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