Tuesday, June 3, 2014

The Thomas and Judah Farrell DNA Project: First try at chromosome mapping and GEDmatch is down

I love GEDmatch and my most serious DNA analysis work is done there. Sure, it's fun to contact DNA cousins at 23andMe or AncestryDNA but I really need a good chromosome browser and GEDmatch is the ticket. But today it's down and right at a critical junction when I badly need the use of its tools and it's going to be down for a couple of weeks. Grrr.

Now that I've moaned and groaned a moment let me tell you what I'm up to. Cousin Rich and I have about a dozen or so people in various states of DNA match. Mom and Uncle Sonny are the most solid match and share the most DNA. They both descend from the two oldest daughters of Thomas and Judah Farrell. (You can read the overview of the Farrells and this project here.) Mom tested with 23andMe and Uncle Sonny and his sister Aunt Mary tested with AncestryDNA. Mom has now tested at AncestryDNA too. Rich and I have kept a list of DNA cousins and some have good trees and some don't. One guy is adopted so we don't know how he fits in. But they all have some matching segments shared with Mom and Uncle Sonny.

Mom and Uncle Sonny are our "benchmarks" because they share the most DNA. Here's a look at the chart GEDmatch whipped up for us showing exactly how they share their DNA. Nice, huh?

Chromosome browser from GEDmatch.

As each new DNA cousin popped up an idea kept forming and reforming in my noggin. I could see the relationships and the stream of chromosomes, but a pattern wanted to form but just couldn't. Ever have that happen? Now let me tell you how I stumbled into exactly what I needed.

First, I saw that there were two terms and that I might have confused: chromosome browser and chromosome mapper. What you see above is a chromosome browser. It is a tool that lets you compare the DNA of two or more individuals to see exactly which segments of DNA are shared. You can then introduce a third person into this mix and that's called triangulation. If you have three people sharing exact (or very close) chromosome segments, that's called triangulation and with solid trees for all three and only one shared most recent ancestor, it's a sure bet that the chunk of shared chromosomes came from the shared ancestor.

A chromosome mapper is a spread sheet that shows you which segments on which chromosomes are shared between many people. In this way you can determine which chromosome segments came from which ancestor with even greater confidence. With any sort of luck, you can then know that anyone with those exact segments descends from that same ancestor. Yes, that's right. If an adoptee who knows nothing about his ancestors also shares those specific segments they descend from that common ancestor.

Chromosome mapping spreadsheet using a Kitty Cooper template with our DNA matches.
Thank you, Kitty Cooper!!!
You need to know that I have never used Excel before, and it kinda scared me. Looked too complicated. Never mind, because I wanted to do this mapping thing so bad I just jumped in the Excel water. I went on ahead and downloaded a template from Kitty Cooper which you can find here. It's the CSV one. I googled how to use Excel and played with it for a while and found out that I could enter any value in a column and then use Sort and Filter on the Home bar to get the numbers in numerical order. Sounds way, way harder than it is. (Cousin Rich is a whiz at spreadsheets and he'll have a good laugh at my expense reading this! He's in Scotland with family playing golf so maybe he'll miss this post.)
Next step was to decide what the column heading should be. You can see the ones I chose but now that I've played with it, think I'll add "number of generations to MRCA" or most recent common ancestor. See post before this for an overview of our requirements and that should tell you why this is important. There are two columns that you don't see here and those are GEDmatch kit number and email. And obviously you can see the attempted redaction of surnames. Not pretty but it works. 
There are two names that don't have any MRCA or most recent common ancestor info and they are Stephen and David. One is adopted so he came to our DNA matching party with no tree. What we can now tell him is that he shares some of the DNA that came down to us through the Thomas and Judah Farrell pairing. It could be DNA that came with them from Ireland and thereby came from ancestors "upstream". Or it could have come to him from one of the other of Thomas and Judah's children. We just don't know. But he's real family to us.
The second name without a MCRA has a nice tree and ancestors who lived about 10 to 15 miles from where Thomas and Judah lived in what's now West Virginia. We have yet to find our shared ancestor and connect our trees. He's one of us but we don't know exactly how.
There's more to this spreadsheet than you can see here. I have some names and GEDmatch kit numbers but not too much more than that ... because GEDmatch is what I need right now and it's down. Again. GEDmatch, I love ya but you're about to drive me crazy!
The GEDmatch web site says that they are moving to new servers and once that's done the world will be bright and new because the new servers should increase reliability. It's going to take a couple of weeks. Ugh.
The old railroad overpass on the Potomac River near what was once Magnolia, Vest Virginia, home of the Farrell, House, Hartley, and Biggerstaff families who are the subjects of this DNA study.

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