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DNA Painter – Chromosome Sudoku for Genetic Genealogy Addicts

Roberta Estes

Not long ago, Jonny Perl introduced the free online tool, DNA Painter, designed to paint your chromosomes. I didn’t get around to trying this right away, but had I realized just how much fun I would have, I would have started sooner.

Fittingly, Jonny, pictured above, won the RootsTech Innovation award this year for DNA Painter – and I must say, it’s quite well-deserved.

Congratulations Jonny!

I’ll tell you right now, I haven’t had this much fun in a long time!

Want to hear the best part? You don’t have to triangulate. DNA painting is “self-triangulating.” Yes, really!

Let’s get started!

Introducing DNA Painter

To begin to use DNA Painter, you’ll need to set up a free account at www.dnapainter.com.

Read the instructions and create your profile.

Jonny provides an overview.  Don’t get so excited that you skip this, or you won’t know how to paint correctly. You don’t need to be Picasso, but taking a few minutes up front will save you mistakes and frustration later.

Blaine Bettinger recorded a YouTube video discussing how to use DNA Painter to paint your chromosomes to identify and attribute particular segments to specific ancestors. It includes a mini-lesson on chromosome matching.

I strongly suggest you take time to watch Blaine’s video from the beginning. For some reason, this link drops into the video near the end, but just slide the red bar back to the beginning.

Get Started

Here’s my blank, naked chromosomes. Notice for every chromosome, you see a blue paternal “half” and a pink maternal “half.” That’s because everyone gets half of their autosomal DNA from their father, and the other half from their mother.

Looking at my own chromosome painting today, below, it’s incredibly exciting for me to see 57% of my DNA painted, attributed to 77 couples and one endogamous group, Acadians. This took me a month or so working off and on.

At the end of the day, this is often how I rewarded myself! The only problem it that it has been difficult to go to bed.

Comparatively, I’ve been working on my DNA match spreadsheet, attributing segments to ancestors now for 5 or 6 years, and I’ve never been able to see this information visually like this before. This view of my ancestrally painted chromosomes is so rewarding!

Who To Map

DNA Painter is not the kind of tool where you upload your results, it’s a tool where you selectively paint specific segments of matches – meaning segments on which you match particular people with known common ancestors.

How do you know who is a good candidate to map?

I began with painting my closest matches with whom I could identify the common ancestor.

Not only will painting your largest matches be rewarding as you harvest low-hanging-fruit, it will help you determine if you actually have identified the correct DNA for later matches being attributed to a specific genealogical line. In other words, mapping these larger known segments will help you identify false positives when you have no other yardstick.

Your First Painting

I’m opening a new profile in DNA Painter to demonstrate the steps in painting along with hints that I’ve learned along the way.

I’m going to utilize my cousin, Cheryl, whom I match closely at Family Tree DNA. If you don’t know how to use the Family Tree DNA autosomal tools, click here.

Cheryl is my first cousin once removed, so we share a significant amount of DNA.

I’ve selected Cheryl on my match list, checked her match box, and then clicked on the Chromosome Browser in order to view our segment matching information.

You can see on the chromosome browser that I share quite a bit of DNA with Cheryl.

At the top of the chromosome browser, click on “View this data in a table.”

Highlight and copy all of the segments for Cheryl. I only use 7cM segments or higher at DNA Painter, so you don’t have to copy the data in the rows below your last match at that level. DNA Painter takes care of stripping out all the extraneous stuff.

Paint a New Match

At DNA Painter, after you have your profile set up, click on “Paint a New Match.”

Simply paste the segment data into the box in the window that pops up. DNA Painter takes care of removing the header information as well as segments that are too small.

You can click on “overlay these segments” to “test” a fit, but I haven’t really found a good use for that, because I’m only painting segments I’m confident about and I know which side, maternal or paternal, the match is on based on the known relative.

Click on “save match now” in the bottom right corner.

In the Save Match popup, shown above, I utilize the fields as follows.

I enter the name of my DNA match, followed by their relationship to me, followed by the source of the match. In this case, “Cheryl <lastname>, 1C1R, FTDNA”

In the “Segment/Match Notes” I list how the match descends from the common ancestral couple, a GedMatch ID if known, and anything else pertinent including other potential ancestral lines in common. This means that I list every generation beginning with the common ancestral couple and ending with the tester.

Hiram Ferverda and Eva Miller, Roscoe, Cheryl, GedMatch Txxxxxx

You’ll wind up eventually rethinking some of your segment assignments to particular ancestors and you’ll want as much information here about this match as possible.

Moving to the next field, in the “Ancestors Name,” I utilize the couples name, because at this point, you can’t tell which of the two people actually contributed the DNA segment, or if part is from one ancestor of the couple and part is from the other. If the male ancestor is a Sr. or Jr., or is otherwise difficult to tell apart from your other ancestors, I suggest entering a birth year by his name. This is your selection list for later painting segments from the same ancestor, so you want to be sure you can tell the generations apart.

Next, you’ll select the maternal or paternal side of your family. Change the color if you don’t like the one pre-selected to assign to segments descending from that couple. Originally, I was going to have pinks or light colors for maternal, and blues or darker for paternal, but I quickly discovered that scheme didn’t work well, and I had more ancestors than I could ever have imagined whose DNA I am be able to map and paint.

Therefore, pick contrasting colors. You can use each color on each half, meaning maternal and paternal, since the segments will be painted on different halves of the chromosome.

In the “Notes for This Group,” I add more information for the couple such as birth and death dates and location if I know or am likely to forget.

Click “save.”

Here you go!  Isn’t this fun!!!! Cheryl’s segments that match mine are painted onto my chromosomes!

At the right, your ancestor key appears with each ancestor to whom you’ve assigned a color key.

So far, I only have one!

Want to paint another group of segments?

Let’s paint Cheryl’s brother.

Following the same sequence, I paint Donald’s DNA, but this time, I select “Or link these segments to an ancestor I’ve added before.”

I select Hiram Ferverda, Eva Miller and save. The segments that I have in common with Cheryl and/or Don will now be displayed on each chromosome.

Looking at chromosome 1, you can see that I match Cheryl and Don on the same segment at the beginning of the chromosome, but received two different segments of DNA on a different portion of chromosome 1, further to the right.

As one last example, I added the DNA from two known cousins, Rex and Maxine, who descend a couple generations further back in time through more distant ancestors in the same line – one maternal and one paternal.

Click on the chromosome number to expand to see all of the painted segments

You can see, looking at chromosome 3 that Cheryl and Don match me on a significant amount of the same large pink segment plus a smaller pink segment at the end

Rex (yellow) and Maxine (blue) both match me on different parts of the chromosome. It looks like there is a small amount of overlap between Rex and Maxine which is certainly feasible, because Jacob Lentz, the ancestor that Maxine descends from is ancestral to the couple that Rex descends from.

By utilizing known matches, and mapping, we can see segments that move us back in time, telling us from which ancestor that portion of the segment descends.

For example, if the blue segment was directly aligned with one of the pink segments, then we would know that the blue portion of the pink segment descended from Jacob Lentz and Fredericka Reuhl.

This is the most awesome, extremely addictive game of ancestor Sukoku ever.

Wanna play???

Here’s how to prepare for my next article where we’ll utilize the various vendor matches to begin painting.

Download and Upload Your Autosomal Files

You’ll want to have your DNA at the most vendor locations possible so you can find all your matches that can be attributed to known relatives and ancestors. You never know who is going to test at which vendor, and the only way to find out is to have your DNA there too.

For each vendor, I’ve provided a mini-tutorial on how to maximize your testing and transfers both monetarily and for maximum matching effect, or you can read an article here that explains more.

There’s also a cheat sheet for transfer strategies at the end of this article.

A technique called imputation is mentioned below, so you may want to read about imputation here. MyHeritage’s initial offering utilizing imputation was problem plagued but has since improved significantly.

Ancestry

To Ancestry – There’s no way to transfer files TO Ancestry, so you’ll need to test there to be in their database. You will also need at least a minimum subscription ($49) to utilize all of the Ancestry DNA features. You can see a with and without subscription feature comparison chart here.

From Ancestry – There is also no chromosome browser at Ancestry. In order to use DNA Painter, chromosome segment information is required, so if you test at Ancestry and want to paint your segments, you’ll need to download your DNA file to either or all of:

Family Tree DNA

To Family Tree DNA – You can upload the following vendor files TO Family Tree DNA.  Matching is free, but to use the advanced tools, including ethnicity and the chromosome browser, you’ll need to pay the $19 unlock fee. That’s still significantly less than retesting, especially for files that are 100% compatible.

From Family Tree DNA – You can upload your Family Finder results to:

MyHeritage

To MyHeritage – You can upload the following files to MyHeritage:

From MyHeritage – If you test at MyHeritage, you can upload your files to:

23andMe

To 23andMe – You cannot transfer TO 23andMe, so you’ll need to test there if you want to be in their database.

From 23andMe – If you tested at 23andMe, you can upload your files to the following vendors:

GedMatch

GedMatch is a third-party site that accepts all of these vendors’ autosomal files, with a caveat that the 23andMe V5 kit matches very poorly and requires special handling. I don’t recommend using that kit at GedMatch unless you are matching against other 23andMe V5 kits.

I upload multiple kits to GedMatch and mark all but one for research only. This allows me to use my Ancestry kit to match with other Ancestry users for more accurate matches, my Family Tree DNA kit to other Family Tree DNA kits, and so forth. Not marking multiple kits for research means that you’ll appear more than once on other people’s match lists, and only your first 2000 matches are free. Marking all kits except one as research is a courtesy to others.

Recommended Testing Strategy for New Testers

  1. Test at Ancestry and download to GedMatch.
  2. Test at Family Tree DNA and upload to MyHeritage and GedMatch.
  3. Test at 23andMe and upload to GedMatch Genesis.
  4. At GedMatch, mark all except one kit as “research,” then utilize your kits from the same vendor for one-to-one comparisons.

Recommended Transfer Strategy

Of course, where you have, and haven’t already tested will impact your transfer strategy decision. I’ve prepared the following cheat sheet to be used in combination with the information discussed above.

*Unless you can transfer a 23andMe V3/V4 or an Ancestry V1 kit to Family Tree DNA, it’s better to test at Family Tree DNA. Ancestry V2 tests are only 20-25% compatible.

A transfer from Family Tree DNA to MyHeritage is best because those vendors are on the same platform and the tools at MyHeritage are free.

In my next article, we’ll discuss how to mine your matches at the various vendors to obtain accurate segments for chromosome painting – including a strategy for how to utilize Ancestry and Gedmatch together to identify at least some Ancestry segment matches.

So, for now, get ready by transferring your matches into whichever data bases they aren’t already in. The only data base where I couldn’t identify matches that I didn’t have elsewhere was at 23andMe. The rest were all there just waiting to be harvested!

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Transfers

Genealogy Services

Genealogy Research

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