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If you want to play with the autosomal tools at GEDmatch...

Replies: 24

If you want to play with the autosomal tools at GEDmatch...

Posted: 20 Dec 2012 2:22PM GMT
Classification: Query
Edited: 20 Dec 2012 2:25PM GMT
It dawns on me that some people may want to play with the GEDmatch site and get a feel for things before Ancestry releases our raw data.

Anyone is welcome to use my GEDmatch "kit number" (M201056) to check out some of the features. Kit numbers are hardly a secret (unless you want them to be); I put mine in all of my profiles, so no biggie to me.


Below are some things I would suggest trying, just to get an idea of the features.

(Hopefully URLs are okay since this is a non-profit, non-competing site. If not, I respectfully ask that the moderator simply strip the URLs instead of deleting this entire post. Links can be found on the main GEDmatch page if the URLs are stripped.)


ETHNICITY ("Ad-Mix Page")
http://ww2.gedmatch.com:8006/autosomal/ap_mix1_gen.php

Here is where you blow away the simple notion of the pie charts we get at Ancestry and other places. ;)

On this page, it will ask you to select a project. I definitely suggest trying out several. Some people feel that different projects do a better job at identifying different cultures. However, by trying a bunch of different project settings, you'll quickly see that many just say the same thing in different ways.

Just to start, pick "MDLP Project" then "Chromosome Painting." On the next screen, enter the kit number (M201056) and leave the rest as-is. (Again, you can always play with options later.)

Remember that you get one chromosome from each parent. When I look at, say, the start of my second chromosome, I have to wonder if the light blue ("Atlantic Mediterranean Neolithic" aka W/SW Europe) is coming from one parent and the beige ("Northeast European") is coming from the other. (Fingers crossed that my Dad can test soon and make all of this a bunch easier.)

The variety of color (and labels, if you try some of the other projects and options) quickly shows that saying "You are X% such-and-such" is just not that simple. Here at Ancestry, I'm 75% British Isles, 15% Eastern Euro (a shock to me at the time), and 7% Finnish/Volga-Ural, with 3% Uncertain. Look at my chromosome painting, though, and you can see things like significant spikes of black (North American Indian). Not enough to make the radar at Ancestry, who seem to be playing to safe, but enough to be "real."

If you choose "Admixture Proportions by Chromosome" (instead of Chromosome Painting), you can see that I technically match 21 out of 22 of the suggested backgrounds at this particular project. That certainly adds some spice to my WASPy paper trail! I hope that examining raw data in this way helps people realize how complicated the issue of biogeographical analysis really is. We're talking about thousands of years and a lot of migration.

(I also hope that society becomes a more tolerant place as more people get to see how diverse their backgrounds are.)


BIG LIST OF MATCHES (One-to-Many DNA Comparison)
http://ww2.gedmatch.com:8006/autosomal/r-list1.php

I'd guess that this probably ties with the ad-mix tools for popularity, although the matches are of course *much* more useful for genealogical purposes. Just enter the kit number, leave everything as-is, and press the button.

Kind of makes you miss our pretty interface here, eh? :)

Things to notice:

1. Clicking on "T" in the "Triangulate" column gets you a list of your match's matches who match his/her other matches. (Say that three times fast.) It's only available if people upload their match results in addition to uploading raw data. (Hopefully Ancestry will be similar to other companies and offer a spreadsheet of our match results.)

This is a great tool because sometimes it's your match's matches that have the clues to your common ancestor. However, as I mentioned in another post, I haven't had an easy time with this. It is probably more useful either when you've done other groundwork or have matches with fewer matches so the pages don't take forever to generate. For now it's easier for me to use other options, but that's my failing.

2. You may notice the lack of "G" links, meaning that few people have uploaded GEDcoms. Yep, it's a bummer! If they do have a GEDcom, use the GEDcom matching tool on the main page to compare yours to theirs.

3. Clicking "A" will show you where on the chromosomes you match the other person. (Submit the form as-is.) If you click "A" for my closest match, you can see that he and I share a big chunk on chromosome 8. ********This kind of information is the crux of genetic genealogy********, so we'll get back to this in a minute.

4. The final set of columns has to do with X-chromosome matching. You can only match certain ancestors on the X chromosome. (If you're a guy, your father's side of the family is eliminated right away, because you only have one X from your mother.) X-chromosome matching is fascinating because you can quickly narrow the connection down to particular ancestors. This post has more info and helpful charts to visualize which ancestors "qualify": http://www.thegeneticgenealogist.com/2008/12/21/unlocking-th...


MAPPING THINGS OUT ("Chromosome Browser" and "Show results that match on a given chromosome segment")

I love this part!

http://ww3.gedmatch.com:8004/entry_chrom_match.php

This is similar to segment comparison tools at other companies. With the Chromosome Browser, I can see at a glance if I have multiple matches on the same chromosome segment. I can then compare these people to see if they match each other on that segment. If they do, then we all have a common ancestor that we can hunt for together.

If these people don't match each other, then I know they come from different sides of the family.

http://ww2.gedmatch.com:8006/autosomal/seg_compare1.php

You probably don't want to pull up the whole chromosome browser every time. In the previous section, I pointed out my match on chromosome 8. I could use the segment comparison tool to see who else matched me either just on the entire chromosome or just a specified segment of that chromosome.

At another company, I've identified a common pair of ancestors with a 4th cousin: we'll call them Blah Blah and Yadda Yadda. My shared segment with that 4th cousin is on chromosome 3, 74000000-82000000.

So, I plug that information into GEDmatch's segment comparison tool (linked above):

Kit number: M201056
Chromosome Number: 3
Segment Start: 74000000
Segment End: 82000000
Minimum matching segment size: 7 (a common threshold)

Click "Submit" and I find that I have three matches on that segment. The kit numbers starting with "M" are at 23andMe and the ones starting with "F" are at FTDNA.

Unfortunately, my 4th cousin isn't using GEDmatch. However, I can 23andMe's built-in segment comparison tool to see if he matches the two 23andMe matches. (Luckily I didn't just have the FTDNA match. Also, luckily I've already asked those two people to "share genomes" at 23andMe *and* they've accepted.)

Result: Yes! My 4th cousin matches both of the 23andMe matches.

Next question: Do those 23andMe matches match the FTDNA match I have on that segment?

For this I use GEDmatch's one-on-one DNA comparison (http://ww2.gedmatch.com:8006/autosomal/u_compare1.php) to find out. (I just type in the kit numbers I want to compare. See what I mean about kit numbers not being particularly confidential?)

Nope, no match! Looks like that FTDNA match comes from Dad's side of the family instead. (So, even a non-match provides some new info. Cool, eh?)

I actually match that 4th cousin on four different chromosomes, each time with segments of significant (> 7 cM) size. I only match those other people (who are parent and child, as it turns out) on one chromosome. By continuing to make comparisons and eliminations, we'll hopefully be able to map that little chunk of chromosome 3 to a place higher up in the tree.

The next step for me is to contact those 23andMe matches to let them know what I've found. "Hey, you and I both match John Doe on the same segment at chr 3. John Doe and I are both descendants of Blah Blah and Yadda Yadda. Here's a link to their ancestors. Do you see a connection to your own tree?" (At Ancestry this will be SO much easier because we have the best tree-sharing interface here.)

I'm not giving out my GEDCOM number to play with those tools because I need to re-upload my GEDCOM. (Long story. Sorry! If you want to play with tree comparisons, find a GEDCOM number and kit number on one of my matches on the big list.)


This is just a slap-happy tour of a few GEDmatch features that I hope will inspire people to get excited about what the next level of our Ancestry DNA experience will (hopefully) be.

(But as I've said in other posts, I *really* hope Ancestry implements their own versions of these tools. Getting people to use GEDmatch is going to be a challenge. Email or call Ancestry and let them know what you want!)
SubjectAuthorDate Posted
Shari S. 20 Dec 2012 9:22PM GMT 
sherburl 20 Dec 2012 10:07PM GMT 
DPotts57 21 Dec 2012 3:28PM GMT 
mi2early 21 Dec 2012 4:22PM GMT 
DPotts57 21 Dec 2012 5:11PM GMT 
Donna westwoo... 21 Dec 2012 4:27PM GMT 
jbarry6899 21 Dec 2012 4:35PM GMT 
cyndi308 22 Dec 2012 12:20AM GMT 
Nachalink123 22 Dec 2012 2:40AM GMT 
JSandelW 6 Mar 2013 2:28PM GMT 
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