How To Use The 3D Chromosome Browser On GEDmatch

The 3D Chromosome Browser is one of the two chromosome browsers in the free set of GEDmatch tools.

You’ll either love the 3D display or find it less useful than the 2D options. It’s worth testing the 3D version on different scenarios to see if it suits your research.

I’ll run through a specific scenario of evaluating multiple kits in this article.

What Is A Chromosome Browser?

Never mind 2D or 3D, you may be wondering what on earth is a chromosome browser? If not, skip to the next section!

A chromosome browser displays shared DNA segments between kits in a visual layout across chromosome pairs.

A 2D Browser

This is easier to describe with a picture in 2D.

The picture below shows just a single chromosome from the chromosome browser in the One To One Comparison Tool (part of the free tier). I’ve marked up the display with some text descriptions.

single chromosome bar in the one-to-one comparison tool with blue shared segment highlighted

The blue bar is how GEDmatch highlights the shared segments of DNA that are long enough to be significant.

This a nicely colored display, but it’s not particularly helpful. Things get more interesting when you compare three or more DNA matches with a chromosome browser.

In the example below, three kits have overlapping sections of shared DNA on the 16th chromosome pair (this display is from the paid tier).

Notice how the segments overlap. This could be due to our four kits inheriting DNA from  a shared ancestor.

But before I jump to conclusions, I must take a drawback of the chromosome browser into account.

Paternal/maternal chromosome pairs

One of the drawbacks with most chromosome browsers is that they don’t distinguish between your paternal and maternal chromosomes in a pair.

This means that two of these matches could be on my maternal side and the other on my paternal side. In other words, the entire group may not descend from the same ancestors.

So, overlapping groups require further investigation. But they’re a great place to launch your research.

Genealogy Quotes By Writers x
Genealogy Quotes By Writers

3D Browser Versus 2D Browsers

GEDmatch has one version of the 3D Browser, and it’s part of the free tier. In contrast, there are several different 2D Browsers.

The 2D Browser on the free tier is part of the One-To-One Comparison tool. This means that you can only run it on two kits.

The difference with the 3D Browser is that the 3D version takes from three up to ten kits.

The paid tier has several different 2D browsers that also take multiple kits.

Preparation For Using The Browser

The 3D Chromosome Browser requires you to enter a list of three to ten kit numbers. So, before you launch the browser you should prepare a list of target kits.

Usually, one of those kits will be your own and you’re trying to identify small groups of DNA relatives who belong to the same branch in your family tree.

The easiest path is to start with a group of matches that you suspect share the same ancestors.

The easiest way to collect possible groups with the free tier is through the “People Who Match Both Kits” report.

I have a separate tutorial on viewing shared matches on GEDmatch. Here, you can follow through my worked example.

Try to start with one or more known relatives

In the example for this article, I’m starting with a match named Marie. I already know our common ancestors. This was through examining her family tree.

We share about 30 cM and are 3rd cousins once removed That’s quite distant, right? Let’s see how the scenario plays out.

Prepare a match list

I ran the “People who match both kits” tool on my kit and Marie, my known relative.

Now, I’m simply going to take the top four matches in common. You could be a bit more selective here e.g.. only taking matches who have a family tree on GEDmatch.

There’s no simple way through the free tier interface to plug your selected matches into the chromosome browser. Just copy the kits to a spreadsheet or a text file.

For this worked example, these are the four kits (aside from my own):

  • Marie 30 cM
  • *TM  30 cM
  • Vicky 24 cM
  • Charles 24 cM

These are quite low matches, but that’s what I have to work with.

You’ll find other articles with examples of using siblings or close cousins in the comparisons. I don’t have that option.

Check which chromosomes are involved

If you’re working with distant matches like this example, I suggest that you run the One To One Autosomal Comparison tool on your known relative. This will identify which chromosomes are of particular interest.

This is the result from our example:

In this case, Marie and I share DNA on the 16th chromosome. Knowing the specific chromosome(s) will be useful later.

How To Use The 3D Chromosome Browser

When you open the 3D Chromosome Browser from the free tools section, you can enter up to ten kit numbers on the parameters page.

Don’t forget to include your own kit – I often forget and then spend a few seconds blinking in confusion at the results.

The final input box on this page lets you change the minimum cM threshold from a default of 7 cM. I’ve kept the default for this worked example.

Submit your request via the “Display Results” at the bottom of the page.

Tabular results

The first set of displayed results are several tables that summarize the comparison data.

You don’t need to pay much attention to this display right now, although we may come back to it later.

The point about the 3D chromosome browser is to translate these raw numbers into a visualization.

Click the “HERE” button at the top of the page to run the visualization.

3D Display with no shared segments

The 3D display opens with a visualization of Chromosome #1.

If none of the matches share a segment on Chromosome #1, then your display will look like mine below.

Notice how there are parentheses around the number 1 in the drop-down menu. This also tells me that this chromosome pair has no shared segments across the five DNA kits I’ve chosen.

It’s important to understand that the Chromosome Browser is looking for shared segments between any two of the DNA matches you listed. It doesn’t matter if one of those kits is yours or not.

Find a chromosome pair with shared segments

The drop-down box at the top lets you pick a chromosome pair from the list.

Notice how there are no parentheses around chromosomes #2,4,5,6, and 11. There’s no point picking these chromosomes as there are no shared segments to show.

I already know for this example that I want to focus on Chromosome #16. So, I choose this from the drop down.

Viewing the default rotation angle

The chromosome display opens with the 3D visualization at a default angle.

This picture shows the left hand side of the screen with the kit numbers and names. At a glance, I can see that only four of the five kits are represented on this chromosome. These four kits have their names in white text.

The entries for Vicky are greyed out. So, now I know that Vicky doesn’t share DNA with me on the 16th chromosome, even though she is a match in common between myself and Marie.

If that’s confusing, I’ll tell you that Vicky matches with me on chromosome #4 and she matches with Marie on #17. I checked this through the One To One Autosomal tool.

Now, we’ll take a look at the full default display. There are four areas of shared DNA toward the higher positions on the chromosome pair.

But are all the shared segments all overlapping? It’s hard to tell with this angle.

Perhaps it would be easier to see if the display was rotated. Now it’s time to play with the sliders at the top of the screen.

Use the X and Y axis rotation sliders

Everything may be clear to you with the default display. But if you experiment with the rotation, you may find a clearer view of the overlapping sections.

In the picture below, I left the X-axis alone and I increased the Y-axis. When the display is almost horizontal, it becomes clear that three of the matches overlap at a specific position and one does not.

Notice how that the section in blue seemed to overlap in the default display but is more clearly separated in the rotated display.

This is why you should experiment with the angles.

The other point I’ll make here is that the clearest angle was when the display was near horizontal. Or course, this is the closest it gets to being a 2D display!

So, why not just go with the 2D display? Because the multi-kit 2D chromosome browser is only available in the paid tier!

Don’t be confused by visual distortions

Another point to notice is that the blue section is significantly longer than the two green sections in the visualization.

However, the color legend at the bottom of the page shows you the ranges of cM involved. Blue sections are 5-10 cM while green sections are 10 to 20 cM.

The segment display is not to scale, so don’t let that fool you.

Figuring out which matches are where on this display

You now need to figure out exactly which kits are contributing to the overlapping colored sections.

For me, this is the trickiest aspect of using the 3D chromosome browser.

In my example, the segments of interest are near the end of the chromosome display. I moved the X axis above 180 degrees to flip the kit number and names to the far end of the display.

I’m showing the screenshot below simply to illustrate that it’s a different angle again to the one I used to identify the overlapping matches.

My goal in this step is to identify the matches that are represented by the intersection at the two green and one yellow sections in the display.

Optional step: check back with the tabular results

You’ve rotated and squinted at the screen, but still find it difficult to line up the kit numbers with the colors?

This is where it can be useful to press the back button and take a look at the tabular data. Specifically, examine the “Segment Details” at the bottom.

In my example, I had identified that two green and one yellow intersections were overlapping in one area. But the blue section was an outlier.

Check out the blue section in the “Segment Details” table below. The blue overlap is between the kits for *TM and Charles.

The From and To positions for this section are from 59K to 71K. In contrast, all the rest start further up the chromosome after position 78K.

Notice that Vicky is nowhere to be seen? We’ve already eliminated her through the visualization.

But I found it difficult to use the visual display to figure out who was involved in the blue section. Now I know its Charles and *TM.

But I share a segment on #16 with *TM. The outlier here is Charles. I don’t share significant DNA with Charles on the 16th chromosome.

I’ve already got rid of Vicky from this potential group, so now Charles has to go!

Verify with the One To One Autosomal tool

The most accurate tool on GEDmatch is the One To One comparison tool. So, the last step is to verify the positive findings with this tool.

In this case, I want to verify my shared segments with *TM.

In the picture below, I’ve lined up the display of the One To One Autosomal Comparison with Marie and with *TM. I did so by opening two browser tabs and taking separate screenshots.

This is another way of looking at what the 3D Chromosome Browser was showing us.

Free Tier Alternative

I’ve already mentioned using the 2D Browser in the One To One Comparison tool. The disadvantage is that it only compares two kits at a time.

In my example, I ran the 3D Browser on five kits. Remember, the 3D browser compares all kits to each other.

In order to get the same comparison with the free 2D browser, I would have had to run the One To One comparison ten times (for ten different combinations of the five kits).

However, this becomes very tedious with repeated use. If you’re going to get into triangulation of your DNA matches, the paid tier tools are well worth it.

Paid Tier Alternatives

In my example scenario, I used the 3D Chromosome Browser to examine the top four matches I have in common with a known distant cousin. I wanted to identify if we five formed a group with a common ancestor.

What if I’d plugged in the same kits into one of the paid browsers? I’ll use my favourite, which is the Compact Segment Mapper. The output is below.

It literally takes me two seconds to see that Marie and *TM have an overlapping section on chromosome #16, while my matching DNA with Vicky and Charles is separate to the others.

Personally, I find the 2D browsers to be easier to use and interpret than the 3D version.

Other Articles And Tutorials?

We have about 30 articles and tutorials covering the many different features of the GEDmatch platform.

Our article on how to use GEDmatch will give you an overview of the site with links to the in-depth tutorials on specific tools.

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