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Important Changes at GEDmatch

If you have not logged into GEDmatch recently, please do so and either accept the new terms and conditions or don’t. Unless you are clearly USA based*, your kits will not be visible to your relatives any more unless you accept. I have linked to numerous other blogs at the end of this article to help you make your choice. I recommend reading either the one from Roberta Estes or EU users, the one from Debbie Kennett. Both look carefully at the new terms and conditions which are not very different from before.

Frankly, I was surprised by the panic expressed last week by some in the genetic genealogy world on FaceBook due to the sale of our beloved GEDmatch DNA tools site to a forensic science company. Personally, I hate knee jerk reactions so I did some research into this company, Verogen, as well as communicated extensively with Curtis Rodgers, one of the GEDmatch founders, and Kim Mohr, a spokesperson for Verogen.

To remind you all, GEDmatch is the best place to compare DNA tests done at different companies to each other or just to see the actual chromosome locations shared by two Ancestry testers. While both Family Tree DNA (ftDNA) and MyHeritage accept uploads of tests from other companies so you can compare on those sites, neither has the extensive tools of GEDmatch. FtDNA compares down to very small segments which can be useful in a family project but leads to inaccurate relationship estimates. MyHeritage does not show the X chromosome and neither company shows the fully identical segments (FIRs) that full siblings will have, which can be so helpful (click here).

The DNA Applications menu at GEDmatch

GEDmatch has many useful additional tools, such as “People who match both or 1 of 2 kits ,” an “Are your parents related?” test, the ability to see who matches you on a specific segment, being able to check for full siblings rather than half, and automated triangulation, to name a few of my favorites (click those words to go to that post when I did one or click here for my more general GEDmatch articles). Plus it has GEDCOM comparison utilities. Compare yours to all the ones in the database or to just one other.

GEDmatch became a center of controversy when it was discovered that genetic genealogist Barbara Rae-Venter, working with law enforcement (LE). had solved the Golden State Killer case (click here) using that site. Since that time, there have been more controversies around law enforcement’s use of the site and many overblown scare articles in the press. Personally if my DNA outs a distant cousin who is a murderer or rapist, that’s fine with me. Genetic genealogy techniques are used as a tip; no one is arrested without getting their DNA from discarded materials and seeing if it is a match to the crime scene. I know some people are afraid of the possibility of false arrests, but that just does not happen with these modern techniques. You can, as before, choose to opt out of allowing LE to see your results on GEDmatch when looking for cousin matches to the dna of the perp or the unidentified victim.

In recent months, there have been more problems, news stories and controversies, including a Florida search warrant being granted. One has to feel for the two retired hobbyists who founded GEDmatch to help in their research and ultimately help us all, keeping most of the features free. Clearly getting the site owned and managed by a more professional group would be of great advantage to the users. Curtis spent several months looking for the right partner that would respect the original misson of GEDmatch and yet deal appropriately with LE, the EU, and security issues. He and the programmers, the two Johns, will continue to work on the site as consultants.

So who or what is Verogen? Two years ago this company was spun off from Illumina (the maker of the chips and machines that all the consumer oriented DNA testing companies use to sequence your DNA). It has 50 plus employees and plans to continue growing. Their office is in a small office park near UCSD here in San Diego. Continue reading

Please Opt In at GEDmatch

In these modern divisive times, even the genetic genealogy community has been torn into two camps. Is it modern nature to react with emotion rather than thought? With the “are you with us or them”? Is this what overuse of social media has done to us? I can see both sides of the issue. Some of you may wonder what I am even talking about ….

Cece Moore on Dr Phil explaining how she uses DNA to find criminals (click image to go to that site for the article and video)

The problem has arisen because Law Enforcement (LE) has been using DNA and genealogy databases to help find violent criminals and to resolve many old and cold cases like the Golden State Killer (GSK) case. They are using the techniques and tools that were developed for breaking genealogical brick walls and helping adoptees find their biological families. Personally, I applaud this usage and the closure it brings to the families of the victims. A dear 4th cousin of mine lived in fear during her adolescent years in Sacramento because of the GSK.

However the issues of concern for many genealogists are privacy and consent. Frankly, I think you should not test your DNA if privacy is a worry of yours. So many people have tested now that you can be easily identified if you do it too. My son and two nephews have chosen not test for that reason.

How about consent? Consider the site GEDmatch.com, which was developed to let people compare their DNA tests with testers from other companies, as well as provide many helpful additional tools. If you uploaded your DNA there in the past, had you given your consent for this usage? After the GSK case. I marked all the kits I control as research until each person had responded with permission to open it up. Most were happy with the thought that their DNA might out a distant cousin who was a criminal. Polls show that 90% of Americans are OK with this too.

I have been asking everyone again since GEDmatch now has an specific opt in on each kit for LE usage of those test results in comparisons. There is also an opt in for whether the link to your WIKItree compact tree should show. Both are important. Until many more people have opted in, the benefit of the database for LE is very limited.

Why the opt in now? Why is the genetic genealogy community so divided? What happened?
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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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Getting Started with GEDmatch

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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