DNAPainter – Mining Vendor Matches to Paint Your Chromosomes

This isn’t quite the same as when my mother used to talk about painting the town, but in genetic genealogy terms, it’s better.

This is the second of 4 articles that will describe how to use DNA Painter.

Today, I’d like to talk about how I utilize the various vendor testing tools combined with DNAPainter to “mine my DNA,” or better put, to mine my ancestor’s DNA which is now mine, pun intended.

To review instructions for how to set up and use the DNA Painter tool, please read DNA Painter – Chromosome Sudoku for Genetic Genealogy Addicts and then come back here to proceed.

I’m going to discuss each vendor’s tools and how I’ve used them, sometimes in combination.

57% Painted

Please note that you can click on any image to enlarge

Is this not a beautiful thing to behold? That’s my ancestors, in loving color, looking back at me, on MY chromosomes.

I’m completely thrilled that I have managed to paint 57% of my chromosomes. I’m a visual person, and while I’ve worked with spreadsheets now for years, I’ve officially abandoned them. Ok, mostly.

Yes, you heard me right – I’ve abandoned the spreadsheets in favor of DNA Painter, at least for segments where I can positively identify an ancestral couple. In other words, those segments that can be reliably mapped.

That 57% is made up of 445 segments in total, split between my maternal and paternal sides. That’s without counting my mother’s DNA. While I do utilize matching to my mother in order to be sure that a match is really a valid match, I didn’t paint her DNA. Obviously, I’m going to match her 100%, and DNA painter already breaks chromosomes into my pink maternal and blue paternal sides.

Key Elements

  1. The single best thing you can do in order to paint your chromosomes is to have known family members and cousins test. You can then paint their DNA that matches yours, attributing it to their identified family line.
  2. The second best thing you can do is to work with your matches using their trees to identify your common ancestor.

Now, you’re ready to begin painting.

I’m going to step through the process I used at each vendor to identify paintable segments.

I did not paint segments that I could not identify to an ancestral line, except for my endogamous Acadian line which I labeled simply as Acadian to mark those segments that I can identify as Acadian, but I can’t identify a specific ancestor, or ancestors. When I can identify the Acadian ancestor, I paint that segment using the ancestors’ names.

Family Tree DNA

At Family Tree DNA, I begin with my closest matches that are not immediate family – meaning not my parents, children or grandchildren. I’m looking for aunts, uncles, cousins, etc. I don’t paint siblings, but often half siblings are extremely useful because they can help you identify which paternal side other matches are related to.

In the first DNA Painter article, I explained how to utilize the Family Tree DNA chromosome browser to select an individual whose matching DNA can be displayed so that you can copy and paste that segment into the painting feature of DNA Painter.

On your results page, your “bucketed individuals” who have been assigned as maternal (pink icon above) or paternal (blue icon not shown) can be a huge clue when used in conjunction with the in-common-with (ICW) tool and the matrix.

You can also search by ancestral surname and then evaluate each match through common surnames, trees and other resources. If you’re not familiar with how to use the tools at Family Tree DNA, here’s a quick run-through.

Select the individual whose DNA you wish to paint, view in the chromosome browser, then copy and paste from the grid below to the DNAPainter tool.

I painted the matching DNA of all the people whose common ancestor with me I could positively identify before moving on to the next vendor.

Who Have I Painted?

As you begin to paint segments from multiple vendors, you may wonder if you’re finding duplicates. It’s easy to tell. At DNA Painter, click on “All segment data,” below the legend in the bottom right corner.

This displays the entire list of matches whose DNA you have painted, in spreadsheet format. You can sort by match name or simply do a browser search. (CTRL+F)

You can also download this data into a cvs (Excel compatible) file at the top left of this page.

Avoiding Duplicates

As you view and paint your matches at the various vendors, you may discover that you have already found a match with that person at another vendor, either because they tested there or uploaded their autosomal file. When possible, avoid duplicate painting. It won’t help anything and will just clutter your chromosomes. You may not always be able to identify a match as a duplicate, especially if the tester utilizes a pseudonym at various locations. Don’t’ worry though, because you can always easily delete it later and a duplicate person/segment certainly won’t hurt anything.

Ok, now to our next vendor! Let’s find more segments to paint.

MyHeritage

At MyHeritage, click on DNA matches.

At the right of the search box, fly over the little pink key (or funnel) looking thing and you’ll see the option for “Has Smart Matches.” That’s what you’re looking for.

Click on the key icon.

Smart Matches mean that your DNA matches and you have a common ancestor in your trees. Click on the purple button to review this DNA match.

For each match, scroll all the way down to the bottom where your matching chromosome segments will be colored.

At the right, above the chromosome browser, click on “advanced options” which will allow you to select “download shared DNA info.” You need to download to your system so that you can copy and paste the matching segment information to DNA Painter.

MyHeritage has a few more columns than necessary, and DNA Painter can’t utilize them. Delete the columns for Name, Match Name, RSID beginning and end, and also eliminate SNPs due to an overestimation issue. In many cases, the SNPs at MyHeritage are twice or more than the number of SNPs when comparing the same segment at other vendors.

Now that your segment is cleaned up, copy the entire group shown above, minus the yellow columns which you’ve deleted, and paste into the DNA Painter spreadsheet.

MyHeritage has recently added a triangulation feature, shown at the far right, below, indicating that these two people individually triangulate with me and Alberta. The icon at far right of “5th cousin” indicates triangulation.

By clicking on the triangulation icon, you then see how that person triangulates with both your match and you – in this case, me, Alberta, and Chandler.

You may choose to paint triangulated segments, BUT, the size of the triangulated segment is often going to be smaller than the amount of DNA than you match individually to either one or both people.

In the example above, you can see that you match the pink person on a significantly longer segment than you match the tan person. The amount of DNA where you match both the pink and tan person is smaller yet, because the area where you match the tan person extends beyond where you match the pink person and vice versa. If you were going to paint ONLY the triangulated segments, you would paint only the portion that is both pink and tan, “boxed” above.

I don’t recommend painting ONLY triangulated segments, because you’ll be depriving yourself of the ability for each person to match others on the portions of the segments on which they match you, but not the other person in question.

In this example, utilizing DNA Painter, you’ll see that people in fact match you AND the pink person on several segments. The segment shown in pink, at MyHeritage, above, is shown on chromosome 5 in DNA Painter as the long mustard colored segment. Look at how many people match you on that segment. This is why we don’t paint only the triangulated portions of the chromosome. That long mustard segment match will triangulate with many people on smaller portions of that mustard segment, as evidenced by the yellow, grey, blue, cinnamon, purple and red segment matches..

DNA Painter helps you triangulate, so there is no reason to restrict your painting to triangulated segments.

Triangulation is a great tool, but don’t mix triangulated segments with matching segments in the same profile, at least not until you get the hang of the tool and using the multiple vendor’s results.

23andMe

Unfortunately, 23andMe doesn’t have tools like tree matching (MyHeritage) or maternal/paternal phasing (Family Tree DNA,) but they do allow testers to enter common surnames.

Looking at closer matches, meaning first, second or third cousins, if they list even a few surnames, you may well be able to identify the common genealogical line, especially in conjunction with ancestral locations and the other people you match in common.

Sometimes you can glean enough information to identify your common ancestor. In this case, even if I didn’t know Cheryl, the surname would have identified the ancestor. If that didn’t do it, the “in common” list below would!

Once you’ve identified the common ancestor and decide you’re ready to paint, click on the Tools tab at the top of your page and select DNA Relatives.

On the DNA Relatives tab, click on the relative whose DNA you wish to paint. I’m selecting my cousin, Cheryl.

Click on the blue DNA Comparison, in the upper right hand corner.

On the comparison screen, you will select yourself as one person and Cheryl as the other.

At the top you’ll see the two individuals and their overlapping segments painted onto chromosomes. Scroll down and you’ll see the segment detail, below.

Highlight the rows (they’ll turn blue, like above) and right click to copy the segment information.

The next step is to drop the results into a spreadsheet, just long enough to delete the first and last columns, shown in red below, then copy the remaining rows and paste into the DNA Painter tool.

Mining Ancestry Data at GedMatch

GedMatch is somewhat of a special case, because GedMatch doesn’t do DNA testing, but provides an open sharing platform by facilitating uploads of raw autosomal files from multiple other vendors. Therefore, anyone with results at GedMatch tested elsewhere. If you tested at all of the other vendors, it’s probable that you find people at GedMatch as a match that match you at other vendors too.

Because 23andMe does not support the uploading of Gedcom files, if your match has uploaded a Gedcom file to GedMatch, or connected to Geni or WikiTree, then you may be able to identify your common ancestor at GedMatch that you were not able to identify at 23andMe.

Conversely, if you match at Ancestry, you won’t be able to paint from Ancestry, because Ancestry does not provide segment information. We will talk about Ancestry as a special case next, but for now, let’s focus on how to utilize GedMatch.

At GedMatch, you’ll work in steps after setting your account up and uploading your raw data file from either:

If you tested elsewhere, or after August of 2017 at 23andMe, you will have to upload to a special section called GedMatch Genesis. GedMatch Genesis provides a sandbox area for files other than the ones listed above that are generally incompatible with those files and with each other. Genesis files often have few SNP locations in common and not enough to match reliably.

I do not recommend DNA painting utilizing segments from GedMatch Genesis.

GedMatch is currently merging their regular GedMatch service with the Genesis service, so I’m not entirely clear how you will tell the difference between the kits known to match reliably, mentioned above, and others after the merge.

Currently, kits with T prefix (Family Tree DNA), A (Ancestry) and M (23andMe) show version levels in the type field when you match in regular GedMatch. MyHeritage kits are processed by the Family Tree DNA lab. G kits used a generic upload, so you can’t tell where they originated.

Kits uploaded in the Genesis sandbox seem to be assigned double alpha letter kit prefixes at random. Genesis includes a “Testing Company” field which does not include a version number. Today, just stay with the regular GedMatch one-to many and one-to-one matching for DNA Painter.

First, you’ll want to perform a one-to-many match.

This page shows your closest 2000 results. In my case, truncating my matches at 12.7cM. This means if I want to see my results below 12.7 cM, I must subscribe to the Tier 1 Utilities in order to be able to display over 2000 matches.

We’ll discuss how to utilize Tier 1 matching in the Ancestry portion, next, but for now, we’ll just be working with the regular one-to-many matches report.

Of course, trusty cousin Cheryl has results here as well.

In order to compare Cheryl’s results to my own, I need to do two separate things:

  • Click on the A link under the Autosomal Details column (above) and/or
  • Click on the X link under the X DNA column

These two results, both of which are paintable, do not display together so must be selected separately.

By clicking on the A or X, GedMatch will display a one-to-one comparison. I leave this page (below) at the default values and simply click submit.

Your next screen will be a match grid.

Once again, select and copy the results, then paste into DNA Painter. If you also have an X match with this individual, return to the one-to-many match page and then click on the X link to repeat the same process for the X chromosome.

Ancestry Through GedMatch

As far as I’m concerned, the best thing about Ancestry matches is DNA shared ancestor hints (SAH) – meaning those green leaves visible near the green “view match” button which indicate that you share both DNA and a common ancestor(s) in your trees.

Followed immediately by the worst thing which is that Ancestry provides no segment data. However, pairing Ancestry with GedMatch can provide you with some segment information, although you do have to dig. That digging was certainly worthwhile for me, as I found several readily identifiable matches.

When I find a green leaf shared ancestor hint at Ancestry, I record as much information about that match as I can in a spreadsheet. The reason is twofold.

  • Ancestry hints tend to come and go, rather inexplicable, and I want to have that information someplace besides at Ancestry
  • I want to be able to view how many matches I have through specific ancestors which I can do in a spreadsheet by sorting.
  • I want to be able to mine GedMatch for segment information for people at Ancestry who have uploaded to GedMatch.

Note the RJE V2 results, a 6th cousin who I match at 6.6 cM, as we’ll be using that at GedMatch.

I maintain several columns in my Ancestry Match spreadsheet, as shown above. I track people who might be good Y or mitochondrial DNA candidates, as well as GedMatch numbers or other useful information.

I don’t utilize segments smaller than 7 cM for DNA Painter, BUT, Ancestry almost always under-reports the matching segment size due to their internal process which removes some segments that do match. Therefore, I search for all Ancestry matches in GedMatch and paint them if they are 7cM or over at GedMatch. You will match at Ancestry down to 6 cM. Since 7cM is the default GedMatch threshold, that works out well. I don’t find them if they are under 7cM at GedMatch, and I don’t care.

In my case to obtain segments smaller than 12.7 cM, because that is the cutoff where the free one-to-many GedMatch tool reaches the 2000 match threshold (for me,) I need to utilize the Tier 1 subscription utilities which are well worth every dollar.

The one-to-many match looks quite different for the Tier 1 tool.

You’ll need to play with this a bit to determine how high you need to set the limit to see all of your 7cM matches. In my case, I had to set it to 20,000.

I utilize two monitors, so I display my Ancestry spreadsheet on the first monitor and the GedMatch one-to-many match table on the second monitor.

Then, utilizing the browser’s search function, I search for any identifiable portion of the information for the Ancestry match at GedMatch.

In the first example, the user’s name is RJE V2. I search at GedMatch for “RJE” using “ctrl+F” which is the browser’s find function.

You can see that the search found a total of 3 different “RJE” entries. Looking at the first 2, you can see that one is labeled V4 and one is labeled V2. Typically, I would look at this and decide that the RJE V2 is the right match based on the user name at Ancestry.

However, look closer.

The RJE V2 at GedMatch has a much higher amount of shared DNA at 3587.1 cM total than the RJE V2 at Ancestry with a total of 6.6 cM. Clearly, this is not the same person, even though the user name is the same.

For all we know, a different person may have used the same user name, which is clearly an alias, noted by the “*”. Or the same person may have multiple kits at GedMatch.

However, in this case, the RJE V2 is not the same match.

However, let’s say that it is the same person and we’ve been able to reasonably identify the match. In order to compare one-to-one, click on the highlighted blue “largest segment” in the autosomal category, shown below.

If you want to compare the X one-to-one, click on the blue largest segment in that column.

From this point, the matching will look the same as the one-to-one GedMatch matching shown in the previous section – so copy and paste as normal.

While this certainly isn’t the most effective way of working with Ancestry matches, it’s really the only hope we have, unless your match has also uploaded to either Family Tree DNA or MyHeritage.

However, in my experience, I generally stand a better chance of identifying Ancestry matches at GedMatch because their user name or the user name of the person managing their account can be found much more readily. People sometimes tend to utilize the same abbreviations, names or nicknames in multiple locations.

Summary

While each vendor has unique strengths and weaknesses today, and GedMatch provides a platform used by some but not all, the best way to effectively paint your chromosomes is to utilize all of the tools available, and sometimes together. I strongly suggest that you test at or upload to each vendor, because you will find matches at each vendor that aren’t elsewhere.

How many segments can you paint on your chromosomes, and what will those segments tell you?

In the next article, I’ll be walking through my chromosome painting gallery to take a look at the hidden messages there! I hope you’ll come along so you can find some hidden messages of your own.

Enjoy!

_____________________________________________________________________

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23 thoughts on “DNAPainter – Mining Vendor Matches to Paint Your Chromosomes

  1. Hello Roberta

    Thanks for the articles on DNA Painter. I have gone through an addiction period of entering as many segments, usually over 15 cM, as I could find and identify. Now that I found all of them, and cant find any new segments to graph, I am undergoing a painful withdrawl

    You dont need to delete the extra information from MyHeritage downloads. I never even noticed until I read your article. I just copied the entire data line and it worked fine. Did that for 20 or 30 MH segments.

    I also found it helpful to order my ancestors in the ancestor box on right with the earliest ancestors on top. So that way if a match to my great gf overlaps a smaller match to my 4th gr gf, the smaller segment for my 4th gr gf appears ‘above’ the longer segment of my great gf. And not buried below the longer segment, where I am not likely to see it unless I go into a special mode.

  2. Hi Roberta, I have been using DNA painter since I saw your first article. I think it’s a great tool but am finding I don’t know enough about my matches. My problem is I don’t have many segments identified for 4th and 5th cousins and those are the ones I would like to map. When I put my two aunts (one maternal, one paternal- my parents are both deceased) they have pretty big matches. I THINK I am at least able to identify which side of the family a person matches on but can’t identify the ancestor. I have one segment identified on my Mom’s side but my only known more distant segment on my Dad’s side is matched with you and your mother on the Miller family line. I’m just trying to figure out if I need to know who the ancestor is first before I put them into the DNA painter or can that tool help me figure out the ancestor?

  3. Addictive! I was glad to see that the application is now web based so I can do it on my iPad. So far, apart from a second cousin and a first cousin once removed, I could not see how I could use this. I eventually found that the best combination is using the DNA+Gedcom matches at Gedmatch focusing on the Ancestry customers and then going back to Ancestry to find out who the common ancestors are. When there is a link on both paternal and maternal side, with some luck, I can identify the origin of the segments by checking which ones my mother does not have, as long as they are not too far back as my parents have several founders in common – some Acadians in the lot as well.
    But it is addictive – the saving grace is the number of people who actually have a tree…

  4. When I started using DNAPainter weeks ago, I kept thinking “I wish Roberta would write about this!” Thank you! I found a trick that has helped me with the Ancestry SAH matches – often you can look at the parents or grandparents of your match and figure out their likely surname (if the parents/grandparents are deceased and names are shown). This has helped me to find them on GedMatch and FTDNA. Also, I have used the DNAGedcom client to download an Ancestry match file, which I then duplicated and edited to be my Ancestry master file. It has my notes for each match already there, and also a column for SAH matches so you can sort for those. Thanks again Roberta for all you share with the community.

  5. Very useful article.
    One problem that I have following the method you described for MyHeritage is that I have almost no smart matches. For example for myself and my two sisters,we have only one Smart Match between us. There is an issue also if you do not have a subscription to MyHeritage. For some matches, their tree will show that we share Smart Matches, and asks me to confirm them. If I click on this, I get a page inviting me to take out a subscription.

  6. Roberta,

    Thanks so much for your articles on DNAPainter…I’m just now beginning to use it and am already hooked!

    Have a question on painting endogamous couples. Both of Mom’s paternal grandparents have close to 100% Mennonite pedigree; I have identified those ancestors back to about 7 generations. Last night I started painting my first Mennonite match who FTDNA lists as “5th cousin-remote”. At 5cM she matched on only one segment of one chromosome; at 1cM she matches 19 segments on 11 chromosomes.

    Luckily, she has posted her tree and I’ve identified 5 pairs of shared ancestral couples but I’m not sure how to paint them since I don’t know which segments belong to which couples. I can see in Family Finder’s “Ancestral Surnames” column that I have a lot of Mennonite matches so wanted to figure out my painting protocol before proceeding any further.

  7. Hi Roberta – this is great. I just started with DNA painter and after reading most of the doc and watching Blaine’s YouTube video, my head was spinning and I was completely befuddled. Then I read your first 2 DNA painter articles and Voila – there was light! I just followed along with you and, while I was reading, I was painting my first two closest matches – a 2nd cousin on Ancestry / GEDmatch from my father’s paternal grandparents and a 2nd cousin on 23&me from his maternal grandparents – a total of 16 segments or approx 5%. As usual, you explained it so clearly and made it so easy. So now I’m off and running on my own.Thank you!

    Barbara Andrews

  8. Hi!
    Thanks for the very helpful articles about how to use DNA Painter. I have now started, and it works beautifully! In all my excitement, I seem to have stumbled on a problem:
    I have a distant cousin, we share about 73 cM, largest segment 16 cM. But I do not know how to “deal” with her regarding to DNA Painter. We are related in at least 7 different lines (all the anscestors are known), and they all end up in 6 different ancestors. The closest one is 7 generations back, and the oldest is 12 generations back.
    Is this cousin suited for mapping in DNA Painter at all, or what should I do? I guess the large amout of cM is do to all the interaction between the people in the area. These are not IBP, as far as I know the segments are not represented in the general population in the area.

    • I have the same problem. I don’t know that there is any “ right” way. I painted all of the possibilities until I could identify the source if each individual segment. Then I removed the others.

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