Tag Archive | GEDmatch

Time to move to GENESIS!

At my recent GEDmatch talk for i4GG, I warned the crowd that soon Genesis would be the only place at GEDmatch where you could upload new DNA kits. Well that day has actually come! Although your kits will migrate from GEDmatch, you may want to upload to Genesis if you cannot wait to see the comparisons. By the way, your GEDmatch login will work just fine at Genesis. Note that Genesis has the GEDmatch logo with an apple core next to it.

So why do you have to move to GENESIS? The problem is that some companies are using newer chips which test for different not completely overlapping markers: LivingDNA and 23andMe since August 2017. Why you may ask? Because the new chips test more SNPs and have more non-European ethnic coverage.

So how do you compare apples to oranges? Well Genesis seems to do a good job of it and the new one-to-many warns you when there are not enough SNPs in common for confidence in the results by highlighting in red. Have a look:

Notice that the last three columns are new. One shows how many SNPs overlap between the kits (in other words, how many SNPs are in common between the two sets of test results so can be compared), the next shows the date compared, and finally the company where the test was done is listed. The latter is needed because kits uploaded directly to GENESIS get assigned kit ids that start with a pair of random letters so the origin is not known from that. Note that migrated kits keep the A,T,M, and H single letters. Also many recently migrated kits will show an overlap of 0 because that has not yet been compared for them.

You may also notice that many columns are missing like haplogroups, gedcoms, and X matching; nor are the columns sortable. Hopefully these features will be added back soon. The display is more compact with the confusing clickable L replaced by clicking on a kit number to see its list of one to many matches. By the way the Tier 1 version of the one-to-many looks exactly the same as the one on GEDmatch.

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New Compact Chromosome Browser on GEDmatch’s GENESIS

Today GEDmatch launched a version of my segment mapper which is integrated with their database. It can be used as a way to easily visualize multiple matches on GENESIS. This first version shows how everyone compares to the first person on the list, like the current 2D chromosome browser but more compact. Also each color is a person.

My Munson cousins in my new compact segment mapper at Genesis

Above is the screenshot of my Munson cousins which even shows one of the boxes that appears when the cursor is placed on a segment. Click on this image to see a copy of the html version (edited for privacy) where you can put your cursor on any segment to see the details. (N.B. when you put your cursor on a segment and the information pops up via javascript that is called a mouse over in geek speak. )

One way to get a display like this at Genesis is to check the boxes (tier 1 only) next to your best matches in the one-to-many (up to 40 of them) and then click the button “Visualization” at the top of the page. Another way to get there is to use the Tier 1 tool “MultiKit Analysis” and select the kits you want to look at. Remember the first kit listed is the one that all the others will be compared to.

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When the DNA says your parents are related

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

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

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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