DNA Painter – Chromosome Sudoku for Genetic Genealogy Addicts

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!

  • This is the first of four articles about DNA Painter. In this article, we’ll talk about how to use the tool, and how to get started.
  • The second article talks about mining your matches at the various vendors for paintable segments with instructions for how to do that accurately with each vendor.
  • In the third article, we’ll walk through an analysis of my painted segments, so you can too – and know how to spot revelations.
  • The fourth article explains how I solved a long-standing mystery that was driving me crazy. If you have a relatively close mystery person in your DNA match list that you can’t figure out quite where they fit, this article is written just for you!

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 – partially compatible with the current Ancestry test chip format – transfer will provide you with your closest matches, 20-25% of the matches you would have if you tested at Family Tree DNA
  • MyHeritage – partially compatible, but uses imputation to infer additional genetic regions
  • GedMatch

My preference is to test at Ancestry, and then test at Family Tree DNA and upload the test results to MyHeritage. The Family Tree DNA and MyHeritage testing platforms are the same, so there is no incompatibility between the two.

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.

  • Ancestry – V1 files generated from before May 2016 are entirely compatible, V2 files from after May 2016 are partially compatible, providing between 20-25% of your matches, meaning your closest matches
  • 23andMe – V3 file from Dec 2010-Nov 2013 and V4 file from November 2013-August 2017 are compatible, the V5 platform file beginning in August 2017 is not compatible
  • MyHeritage – fully compatible

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

MyHeritage

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

  • Family Tree DNA – fully compatible
  • Ancestry – partially compatible but uses imputation to infer additional genetic regions
  • 23andMe – partially compatible but uses imputation to infer additional genetic regions

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:

  • Family Tree DNA – V3 file from Dec 2010-Nov 2013 and V4 file from November 2013-August 2017 are compatible, the V5 chip beginning in August 2017 is not compatible
  • MyHeritage – 23andMe – partially compatible but uses imputation to infer additional genetic regions
  • GedMatch – V3 file from Dec 2010-Nov 2013 and V4 file from November 2013-August 2017 are compatible, the V5 chip beginning in August 2017 is only compatible in the Genesis sandbox area. V5 matching is not reliable. Files from other vendors are recommended for GedMatch unless you are matching against another V5 result.

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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44 thoughts on “DNA Painter – Chromosome Sudoku for Genetic Genealogy Addicts

  1. If two persons have a good, credible DNA match (of siblings or close cousins) and the two persons have the same male & female MRCAs; it possible to determine if a matching autosomal DNA segment came from the male or female ancestor? (Assuming the MCRAs have not had a DNA test.)

  2. Wonderful Roberta I also have started to use DNAPAINTER and I love it. I like you description and the way you wright. Looking forward to your coming articles about this wonderful tool. I follow you blog regularly. Thanks for your entusiasm.
    Happy Easter from Sweden.

  3. DNA Painting is Brilliant! On Family Tree DNA I can see how May segments of DNA I match with the significant match. Now, the difference between DNA Chromosome Browser at FTDNA and 23andme Chromosome Browser is that in 23andme I can see who I match let’s say by ethnicity example like My Ashkenazi Jewish are all in that particular segment. DNA Painting in Gedmatch is awesome. Thank you

  4. Thank you Roberta! I’ve been playing around with DNA Painter for a few months now and think I’m getting it but i have a few nagging questions that need answers. I am really looking forward to this DNA Painter series and the answers to my questions that your articles will surely provide. Your blog posts are very much appreciated.

  5. Roberta I also put off playing with DNA painter – I was home sick for two days last week and was able to get on the computer for an hour to play with it. I’m so happy that I did!
    I love the description sudoku for genealogy – so apt! I’ve been thinking in the last few days that DNA matching is like a great big logic puzzle.
    Thanks for another fantastic blog article 🙂

  6. You had me at “self-triangulate.” Have been meaning to try DNA Painter for a while and you’re giving me no excuse to procrastinate! Thanks for the detailed post.

  7. I just started playing with DNA Painter too and am looking forward to your remaining articles about this tool. btw, you and i match at the 5th cousin or greater level. 🙂

  8. How do you know if your Ancestry Raw DNA file is V1 or V2?

    Also, ” partially compatible but uses imputation to infer additional genetic regions” means actually what? I’ve uploaded to MyHeritage from Ancestry. Are some of my DNA matches not valid? Can I not trust what I see in the Chromosome Browser between me and a DNA match? Is a DNA match actually under or over in the amount of cMs MyHeritage shows we share? Am I potentially missing a lot of DNA matches?

    Thanks for another thorough article with great visuals!

    • If you know when you tested, then you know which version. Otherwise, open a copy of the file and it generally says in the first few rows, but you may need to download a fresh copy to upload to other sites. They generally want unopened zip files. Read the article I linked about imputation. They infer DNA that you don’t have by regions you do have. No, it’s not as accurate as testing.

  9. Great article Roberta. Very well written and easy to understand. I began using DNA Painter last week and I’m hooked. I look forward to your next two articles so that I can learn even more.

  10. Thanks for the post. Yes, I agree that DNAPainter is a great tool. So pleased that Jonny Perl’s work has been recognised. After listening to a few talks on “DNA Mapping”, I’ve decided to approach my “painting” differently. I paint by a single ancestor rather than ancestral couple commencing with my grandparents. I don’t paint segments from 1st cousins or their descendants either as the segments I share with them would be painted back to my father and mother (and I know where those segments came from – the full blue and pink lines for each chromosome). Would be interested in hearing any thoughts as I’m still undecided which is the better approach.

    • You don’t have to choose. You can create multiple profiles. I did something like that a couple years ago, but slightly differently. I used the DNA of about 50 descendants of one couple to create a painted map for that couple.

  11. Like several who commented above, I too was standing on the bank of the swimming hole and wistfully watching the other kids having so much fun! I hadn’t yet even dipped my toe in, even! But when one of the kids shouted, “…come on in, the water’s fine!” …well, that was just the encouragement I needed to take the proverbial plunge. 🙂 Thanks for being that kid, Roberta! Now I just hope my internal “Mom” will remind me when it’s time to take a break now and then!

  12. LOVE LOVE LOVE DNA Painter! The visual representation of which chromosome segment came from which set of ancestors is so revealing! I wish I could give Jonny a big hug for providing the coup de grace that has ended my suffering question, “How can I organize all my segment matches, of which I have spend countless hours on, in a meaningful way?”. Looking forward to the rest of your entries for this topic.

  13. Okay, you made me brave enough to try but even after watching Blaine’s video I’m not sure how to make use of some features. I know he said something about being able to see pile-up zones but I’ve forgotten where and he didn’t offer any suggestions about how to make use of that information. I hope that’s something you will do in a future post.

  14. Thanks so much for the push! I am having a ball with DNA Painter. My parents are not related (according to GEDmatch and my best knowledge). But I keep getting messages when I enter a new match that say this person has common DNA with up to four couples that are already entered. It seems my mother’s kin are related to my father’s kin? I am puzzled.
    Couple of questions: What does “group” mean in this? Should I avoid entering cousins with whom I share more than one set of common ancestors?

    • No, it’s not. I like Kitty’s tool, but it doesn’t expand well. This is a different approach. Hers uses a spreadsheet as input, so for people who have performed segment mapping that way, it’s a good option.

  15. I started by putting in my known first cousins, one each side, and my sister. Then I added two groups composed of the people that FTDNA identified as either close maternal matches or close paternal matches. The weird thing I’m seeing in the paint result is that some of the segments from both groups sometimes show up in the same place. That is, some segments from maternal matches have segments that align with those from paternal matches. Am I seeing endogamy in action? Could FTDNA be wrong in their identification? Is there something else I’m missing here?

    • June, that’s just not a question I can answer without seeing what you are describing. You do know that you’ll have people match you on the same segment locations on both sides, right? It’s so easy to talk past each other with descriptions like this.

  16. You could even reconstruct the DNA profiles of your parents, or grandparents this way. Not to get you any more sleep-deprived..

  17. In reading your article, I noticed Samuel Muncey on the chromosome painter. Samuel Scott Muncey, Sr. 1713-1786 is my 5th gg. Is yours the same person or related?

    • I’m guessing that’s the same person. I show him as born c 1712 on Long Island, NY and died after 1798 in Montgomery Co., VA. He was married after 1738 to Mary Skidmore. I would love to exchange information with you. I will e-mail you.

  18. Roberta, you are a BRAT! I have no idea what commitments I have made to anybody for this week, because all I’ve been doing is painting my chromosomes. 🙂 This might be the best thing since whatever the last best thing was…. and I honestly don’t remember anymore. I only have eyes for Jonny.

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