More Automated DNA Match Clustering!

Have you been wondering why are all your favorite bloggers are going crazy for automatic clustering? Well it is a fun visual technique to see which matches belong to which family line by making a chart with your matches across both the top and side, grouping them by who matches who, and then coloring those boxes in. This creates visual clusters which will roughly correspond to your great grandparents or their parents.

My perfect cousin has many matches on all her great grandparent lines (green is my Munson side) so I used her to showcase the new DNAgedcom clustering above. Notice how similar it is to her cluster from Genetic Affairs shown in my previous blog about that site and tool.

Here are all the new ways to cluster our DNA matches:

  • DNAgedcom now has a clustering tool in their client (DGC) which uses your ancestry match list and ICW files (described in detail in the read more below)
  • Genetic Affairs has Ancestry clustering working again
  • DNApainter created a tool to create a CSV from the Genetic Affairs html cluster file. Some of us love to use spreadsheets.
  • Andy Lee of Family History Fanatics figured out how to take an autosomal match matrix from GEDmatch and cluster it in a spreadsheet program, Click here for that video – the explanation starts just after 42 minutes and this is really fun!
  • Rumor has it that GEDmatch may add automatic clustering sometime in the new year…

All of this is based on the method developed by Dana Leeds to organize your matches which is easy and simple to do. Click here for her blog about that.

Read on for how I used the new DNAgedcom clustering tool for myself and my brother, where I know all our great grandparents.

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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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Automatic Clustering from Genetic Affairs

My genealogy groups are buzzing with excitement about a new tool from Genetic Affairs to automate the clustering of your DNA matches. This takes the Leeds method concept to another level.

Everyone is posting pretty cluster pictures like the one below that I made for my perfect cousin, the star of many of my blog posts. This is a table where each DNA match is listed on the top and side; then if they match each other, the box is colored in with the color for that cluster. The chart is sorted by cluster. The idea is that each colored cluster shows descendants from a probable great grandparent couple of yours.

The gray boxes show where people match others outside the cluster which can often happen when families intermarry more than once or when they are first cousins enough times removed to have been in the second or third cousin group by DNA but are related to more than one set of great grandparents.

Automated clustering is useful because it puts your DNA relatives who are related to each other into visual groups so that you can quickly see which line a new match is related on. The picture is pretty but the workhorses are the charts for each cluster shown below that image when you scroll down. Here is the privatized one for my “perfect” cousin showing our MUNSON cluster.

Each name can be clicked to go to that Ancestry match page plus much useful additional information is shown next to the username: how many cMs shared, how many matches shared in the whole group, cluster number, how many people in their tree, and the notes you made for that match.

The image and charts are from the HTML file which arrived via email from Genetic Affairs after I requested automated clustering for my cousin’s Ancestry profile, which is shared with me there. You have to save the html file to your computer and then click on it to view it. When it first comes up, it is a mish-mosh sorted by name, but then it resorts itself by cluster. Fun to watch. Click here for the step by step of how to use this tool from the Intrepid Sleuth. It can also cluster matches from other sites like 23andme.

I decided to try it on an unknown father case I had not gotten around to working on yet, to see if it succeeded in speeding up the process and it did, to under an hour! A new record.

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Fun New Features at Ancestry DNA

I really like a number of the features that have come out recently at Ancestry. My favorite is that the total amount of DNA shared with each DNA relative is now shown on the match list page in centimorgans (cMs). This means that you no longer have to click through to the match page to find that number. Those total cMs are needed in order to look up the possible relationships at the DNApainter calculator. You want to check there because the cousin designations at Ancestry are just groupings based on the amount of DNA and many relationships share very similar cM numbers.

Look at the current top of my 2nd cousin list. These are all children of my first cousins except C.S. who is the grandson of a first cousin. (spot quiz – what is my relationship to each of them? Answer at the end of this article). In each case it shows not only the possible relationship but also the actual cMs and the number of segments.

The other recent feature that I truly appreciate is that Ancestry.com indicates whether there is a family tree linked to the DNA, a tree that is not linked, or no tree at all next to the View Match button. In the past there would only be a tree listed when it was linked to the DNA, so you had to go to the match page to see if there was a family tree that was just not connected to the DNA. A word of warning about unlinked trees, they may not be for the tested person. One of my real second cousins did his DNA test through a friend’s account so he is not in their tree at all!

Did you notice that little blue compare icon under the green View Match button? Click on that to get a comparison of the ethnicity of two tests. It always fascinated me to see the amount of difference between two full siblings. Here I am compared with my brother (click it for a larger version).

A word of warning. A friend complained that his sister only had a tiny amount of XYZ heritage while he had a good 33%. I pointed out that her ethnicity had not been updated to the new version. Once that was done, she had a bit more XYZ than him!

Another benefit of this comparison is the much larger versions of the profile pictures which are on top of the ethnic breakdowns on that page. Space considerations got me to cut them off in my image above. However it is quite nice to get a better idea of what your match looks like than you get from the tiny picture on the match page.

Now for a discussion of the new traits feature …
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Not always a happy ending

Most of the unknown parentage cases I have worked on have had very happy endings and I have enjoyed reporting on them here and in my presentations. Sadly it is not always like that.

My observations from the many cases I have been involved with is that the fathers who never knew are frequently delighted; while the mothers who gave up the child often want to pretend it never happened.

There are at least two cases in my files where the overly young parents, gave up their child, later got married, and were happy to have that child back in their lives. However I have another case where although they later got married, they subsequently divorced and are not acknowledging their son.

A 1960s diary

There are also a few cases where the father claims to not even have known the mother of the child. That does not necessarily stop him from being delighted to have a new daughter or son.

Some fathers are not so welcoming. The first case I ever helped out on was a DNA cousin, early in the days of testing, so I did not know she could be more distant than the reported 4th cousin. Regardless, I was happy to help. She lives in the next town over and came to my house to meet me. I did not realize what an emotional moment it would be for her, meeting her first ever biological relative. Subsequently her birth state opened their records, so she found her late mother’s family. With the extra information from her mother’s diary and her Ancestry test, I was able to find her birth dad, my distant relative. However he said in an email response to her, “Sorry, but I have no recall of a [her mother’s name].” Since the story was one of being taken advantage of when drunk at a party, my cousin chose not to pursue this.

Another genetic cousin who turned up early in my DNA explorations was also more distant than I realized, a double sixth cousin. Eventually I suggested he test at Ancestry where he found a paternal half sister born days apart from him. I found their Dad, my distant cousin, and called him, but he wanted no part of DNA testing. His reason was that he was protecting his known daughter who was going through a tough time and besides he was always “good,” never stepped out. Luckily a few months later that very same daughter did an Ancestry DNA test and is thrilled to have a half sister (she had no sisters) and another brother.

The case that broke my heart was a recent one involving two war babies.

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