Tag Archive | GEDmatch

GENESIS Basics: GEDmatch reinvented part 1

GENESIS.gedmatch.com is a free 3rd party site of tools where you can upload your DNA test results and compare them with those from people who have tested at other companies. It is the new version of GEDmatch.com that can compare the data from many more companies than the original. Click here for my previous post written for GEDmatch users moving to GENESIS. Today’s article is to introduce GENESIS basics to the new tester.

GENESIS Home page for my cousin who has only 2 kits migrated and is not a Tier 1 member

One problem for many users is that this site is not intuitive. GENESIS does not hold your hand and does not build your tree for you. You have to learn how to use the tools there to the best advantage for your own research. I have many posts on this blog for GEDmatch, most of them are also useful for Genesis and I will list some of those later. UPDATE 17 FEB 2019: Click here for the slides from my presentation about the basics of using this site from Saturday Feb 16, 2019, in Carlsbad for the North County DNA Interest Group (DIG).

To get started at GENESIS, you have to be registered as a user. Currently that is still done over on the old GEDmatch.com site. Your login will be your email address with a password you create. Some people prefer to use an email which they have created just for genealogical research. Easy to do at gmail, hotmail, or yahoo, among others and it is a way to create some privacy. Note that GEDmatch is careful to warn you when you register that their site can be used by law enforcement to try to identify violent offenders and victims. Click here to understand how your DNA can out a distant cousin who is a criminal.

Before you can use GENESIS to explore your test results, you have to download your DNA data from your testing company. Click here for the help page that GEDmatch provides on how to download your DNA. The file of your test results is quite large (about 700,000 lines of data) and zipped. DO NOT UNZIP it.

To upload your results to GENESIS you log in and then click on Generic Uploads (23andme, FTDNA, AncestryDNA, most others) in the right hand column under Upload your DNA files. That takes you to a form to fill out before doing the upload. You have to enter the name your kit was registered under, but you can choose to use a pseudonym to appear on Genesis. Put it in the box for alias on this form. For example, all my cousins are called Kittys#CuzNN where the number sign is 1st, 2nd, or 3rd, and NN is their initials so that I know who they are! You have to change the No to a Yes after “You authorize this data to be made available for comparisons in the GEDmatch public database” if you want your results to be visible to your matches.  If you want to stay private, then leave it as is for now, but change it after it is uploaded to “Research” so you can use all the tools on the site but stay invisible. Once your or your cousin’s file is uploaded, you are assigned a kit id (2 letters plus several digits) which will also always show on your home page when you log in. You need a kit id to use the tools. You can upload multiple tests and manage them all from this one user.

You can make edits to any kit you own by clicking the pencil icon next to it on the left side of your home page. Click here for my presentation slide that shows you that edit screen and where to change the privacy to public or research or private.

It usually takes a day or two to fully process your kit so that you can run the most important tool: the one-to-many. That is the tool that lists your DNA relatives in the Genesis database. While you wait you can experiment with the ethnicity tools (called admix here) covered in my Gedmatch basics post and in detail in these slides (click here).

If some cousin, like me, asked you to upload and gave you their kit number, you can do a one to one compare with that kit before your kit is fully ready for the other tools. Click here for the slide that shows the form to make that comparison. There are slides following that one which have some examples. You can use all the defaults when you fill out the form with one exception: you may prefer to check the prevent hard breaks box at the bottom. That is particularly recommended for an X one to one. Personally I prefer to look at the image only comparison first, then I click back and select position only to get the numbers for each segment to put in my master spreadsheet.

Once you see a blue check mark on the line with your kit number on your home page (as in image above), you can run the one to many tool. That looks at all the other kits in the database to find people whose DNA matches yours. The more cMs you share, the closer the match.

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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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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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