Tag Archive | Genesis

More Clustering Tools!

There are many new ways to make those beautiful cluster diagrams of how your DNA relatives are related to each other. Both MyHeritage and Gedmatch GENESIS (tier 1) now have clustering tools (Thank you Evert-Jan Blom). These charts give you an easy way to see your family groupings and can help you figure out a new match since each cluster typically represents a common ancestral couple. Click here for my previous posts on clustering which is based on the Leeds method.

My Dads Clusters at Gedmatch GENESIS

The GENESIS cluster diagram shown above includes the total cM each match shares with you as well as their name and kit number. Click on the “i” in a circle for a pop up box with the user information which includes an email address and whether a GEDmatch tree is linked to this kit. Any of the colored boxes on the graph can be clicked to open a window for a one to one comparison between those two people. Plus you can check the boxes in the select column for any number of matches and then submit them to the multi kit analysis using the orange “Submit to Multi Kit Analysis” button above the name column on the left. To get this clustering tool all you need is a Tier 1 membership and a kit number. It is listed at the bottom of the Tier 1 tools. Personally I like to raise the thresholds to a top 200 and a minimum of 20, but try the defaults first and see what is best for you.

One of the nice things about the cluster output from Genetic Affairs is that it lists all the cluster members in groups below the graph with the number of people in each tree (clickable) and any notes you made on the Ancestry profile. The MyHeritage version also has those cluster lists with your notes and the tree sizes; and of course they are clickable to the match (which may even have a theory of family relativity for you!) and the match’s tree. The down side is that you cannot select the parameters for the clustering yourself, they are preset. Possibly only power users care about that!

Extract from my list of matches in each cluster at MyHeritage

An exciting new feature for those looking for one unknown parent or grandparent is the ability to cluster just your starred Ancestry matches when using the clustering tool at Genetic Affairs.  Click here for my previous post about that tool. There now is a checkbox on the page where you select your parameters for getting a cluster analysis.

Newat Genetic Affairs is the checkbox for only starred matches when starting a cluster analysis

It is a common practice to star (mark as favorites) the matches that seem to be from the family of an unknown parent or grandparent at Ancestry. Usually these are determined by looking at who matches or doesn’t match a close relative like a half sibling or else by eliminating matches from the known side. Sometimes you can use ethnicity. I am currently helping someone where the known side is Jewish and the unknown side is Italian and those are easy to separate.

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Make a combined DNA kit for yourself

Have you ever wanted to make a kit combining all your DNA tests at the different companies so as to get the most SNPs for comparisons? Well GEDmatch GENESIS is now providing that for paid members. So of course I made one of these superkits for myself! I combined my LivingDNA with my V3 23andme and my current Ancestry kit. Now to investigate what I have gained from this.

The first thing I did was compare this new kit to my recent Ancestry kit. All looked fine. It has the expected small differences, many of which disappeared (including the black lines) when I checked the prevent hard breaks box on the form. The older 23andme kit comparison had more black spots and mismatches.

My next thought about my new superkit was that I might get a better comparison to cousins who tested more recently at 23andme but none of them have uploaded to GENESIS yet. So I checked how my comparison to an Ancestry tester, my second cousin once removed Jeanie, looked. The superkit gets the same result as my recent Ancestry kit. When I compared her to my 23andme kit and my Living DNA kit however, there were small differences.

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The Beta One-To-Many Tool: GENESIS Basics II

Finding cousins who can help solve genealogical mysteries are what many of us are hoping for when we do DNA testing. The various One-to-Many tools at GEDmatch Genesis list all the people who match the DNA kit you specify. These are cousins or even closer relatives.

The new beta version of the One-to-Many tool  is found under the heading DNA Applications in the right hand column of your home page.

My red arrow points to it in the image to the left.  It is a much improved tool, more like what was available on GEDmatch. When you click on it, you get a form as shown below which only needs the kit number added.


If you have set up some tag groups (click here for my GEDmatch tag group article), check the tag group box named “All” (shown with my red arrow above). Below is what my One-To-Many result looks like with my tag groups. The kit number is shown with the color of the group it belongs to. Note that when I have a person in more than one tag group, I get duplicate lines for them, one for each color coded tag group they are a member of:

My top matches in the One-To-Many with my tag groups (click for larger image)

One of the great features of this tool is that every column is searchable by putting text in the box above the column and then clicking the enter key. [UPDATE: this is a Tier 1 feature only and is more directly called a filter]. Another one is sortability via the up and down arrows at the top of the column. When working with my Jewish side, I sort by largest segment to get my closest cousins at the top. The reason I do that is that endogamous populations will often share many small segments from way back so the total cM make a triple 5th cousin look like a 2nd or 3rd ; however close cousins will always share larger segments.

This beta One-To-Many tool includes many of the features GEDmatch users are used to: the link to a tree*, the display of haplogroups, the estimation of generations difference, and the X matching. It also includes the new overlap number which lets you know how many SNPs are tested in common between the two kits. The overlap issue was discussed in my previous article about GENESIS

You can click on any kit number to get a One-To-Many for that kit or click on the underlined largest segment number to compare the cMs of the two kits for either autosomal or X. In both cases you are taken to a prefilled in form on which you can make changes to (don’t yet) before you click the Submit or Search button. On the X comparison, I recommend you click the “Prevent Hard Breaks ” because there is a large gap in the middle for many tests otherwise.

New matches will be indicated by having their names and days since upload colored in green. The green gets lighter the longer they are there until it eventually goes away.

Here is a table with an explanation for all of the One-To-Many column headings:

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Basics: GEDmatch reinvented part 1

UPDATE 18-AUG-2019: Since the GEDmatch site and GENESIS are one and the same now I have updated this post to say GEDmatch rather than 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 the new version of the GEDMATCH 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. GEDMATCH 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, . 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 GEDMATCH, you have to be registered as a user.  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 GEDMATCH 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 GEDMATCH 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 GEDMATCH. 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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