How to Use One-to-One Comparison

Video Transcription

So you’ve found your match list on GEDmatch, on the new Genesis system, and now you want to compare your specific kit with somebody else’s specific kit. How do you do that?

Howdy, I’m Andy Lee with Family History Fanatics and this is a segment of DNA. Be sure to subscribe to our channel and click on the bell if you wanna be notified about upcoming episodes in this series. I’m going over each of the tools on the new Genesis system by GEDmatch, and today I’m going to be looking at the one to one matching. Now one to one matching is where you can find detailed information about a specific match. So let’s go over the Genesis system and see how this works. Now, once you’ve logged into the Genesis system, there’s actually several ways you can get to the one to one matching. I’m gonna go through each of ’em just so you know how if we scroll down to the DNA applications, we can see that there is the one to one autosomal DNA comparison and the one to one X DNA comparison.

Now these tools are very similar. The only real difference is is that the X DNA is only looking at one chromosome, the X chromosome, while the autosomal DNA is looking at chromosomes one through 22. When I click on it, it’s going to get me to the Genesis one to one match screen, and you can see what you need is you need two kit numbers in order to use the one to one comparison. Now these could be two kit numbers that you manage or they could be two different kit numbers, but there’s a couple of other ways that are probably actually easier to get to the one to one match screen with a specific match that you want. Now, previously I showed you how you can get to the one to many match screen by just clicking on one of the kits that you manage. And when you do that, it pulls up this information.

If you click on any one of the As in this column, that is going to go to the one to one match screen and it’s gonna have those two kit numbers already filled out for us. Another way to get to the one to one is through the one to many beta, and if we click on that and we put in our kit number, then it will give us our list of matches and we can go down and what we wanna do is we wanna click on either the autosomal number of shared DNA or on the XD that we share with them. Clicking on either one of those also gets us to the one to one screen and it already has the two kit numbers filled in. So once we get to this screen and once we have our two kit numbers filled in, there are several different options of different things to look at.

Now, the first one is the show, whether you want to have the graphics in the position, just the position or just the graphics. Let’s take a look at what each one of those shows. So this first is with graphics and position, and what it does is it goes through each one of the chromosomes and there’s gonna be a little table here with these segments that you share. Then there’ll be a graphic that is displaying what those segments are, and that goes through all 22 chromosomes. At the top is the legend of what each one of those colors mean. Now if I just wanted those positions, I didn’t necessarily want the graphics, I can click on the position only and it will give me just this one table that has all of those segments. So if you are taking segments and making your own table of matching segments, then this is really what you would do because then you could easily copy this whole table, paste it into your program and be able to have those matching segments.

It’s also useful if you use DNA painter in that you can copy those segments and paste that directly into DNA painter to paint your different segments. Now, if you just want the graphic only, then all you’re gonna get is each one of those chromosomes in this little graphic. Now, I use each one of these functions in different ways because sometimes I’m looking at DNA by the tables, sometimes I want to have the computer take those numbers and manipulate them. Other times I’m looking at the graphics for a quick visual of how we might be related. Now that is the basic information. The next option is the builds that you want to display. Whether you want to display build 37, 36 or 38. Now it defaults to build 37, but what this really does is it just changes what the position is for a lot of these things.

So each one of these builds uses a little bit different example, and so the numbers are slightly different. So you can see in this first one, this goes from 14.7 million to 24.2 million, whereas in build 37 it’s 14.8 to 24.4, and in build 38 it’s 14.52 24.0. So a little bit different numbers because they use a different reference set for determining what those numbers are. Overall, the amount of cent Morgans is going to be the same and the amount of snips is going to be the same. Now, normally I just leave this at the default of build number 37, but if you do work with other kits from other companies that may use one of the other builds, then this is useful for actually being able to compare what segment from a build 37 kit is matches up with what segment from a build 36 or a build 38 kit.

The next option here is the window resolution, and this tells you how big you want that graphic to be. Now it defaults at 1000, which is a thousand pixels wide. And so let’s just take a look at the graphics. And on this screen here you can see that a thousand pixels wide takes up almost the whole screen, not completely, but almost the whole screen. If I go back and I change that down to 750, well now my bars are all shorter. They only take up three quarters of the screen. So depending on how big your screen is, if the default is beyond what you have, then you can shrink that. You can also make that larger, and in this case you can see yeah, now it’s much larger. I have to scroll to be able to see where all of those segments are on the graphics part.

The other thing is if you’re really interested in having a single pixel length for each snip, you can click on this full resolution. Now there’s sometimes when this is really useful when you’re trying to pinpoint a specific location on the genome. What is different about this is that this actually has another graphic right underneath it, this white one, which tells you the position. So for instance, 10 M is gonna be 10 million, 10 mega bases, 20 mega bases, 30 mega bases, 40 mega bases, and on. Now each one of these little tick lines, whether it’s red, yellow or green, represents one snip and whether or not that snip is matching between those two people, but you can see that if you do the full resolution, you are gonna get a very, very big long graphic and it’s all dependent on the number of snips. So you can see that some of these chromosomes have much more snips in them than others, and so they’re much longer.

As we go down to our smaller chromosomes, there’s not near as many snips and so they end a lot sooner. But again, if you need to figure out exactly where a certain part is, then this might be useful for you. I really don’t use the full resolution a lot. I usually stick with just the 1000. So next we’re going to get into the snip threshold size. Now what it is to call a match is there’s two things that are needed and that’s what these next two are is the snip threshold and the centor threshold. Now, for a segment to be called a match, it has to match both of these. And so the first one is is it has to have between 200 and 400 snips in a row that match, and then it has to have at least seven cento Morgans in size match.

And so that’s what the defaults are, and you can change that if you would like. So let me just take a look real quick here because I wanna see something that I can change that you’ll see a definite change. All right, so here on chromosome number two, I have a segment that is only 7.90 centimorgans long and it is 834 snips long. And so it’s calling it a match because both of those are above 7 cent of Morgans and above that two to 400 snips. So what if I change this snip limit to 900? Well, now when I go down here, I can see that that segment on chromosome number two is gone because it doesn’t meet my snip limit. It’s still 7.90 cent Morgans, but it doesn’t meet my snip limit. The same thing if I take away that snip limit and I put in, let’s say 10 cent of Morgans when I go down, that segment is still gone on chromosome number two because it doesn’t meet that 10 cent Morgan snip limit that I have.

So where would you want to use these? Well, there’s a couple of cases you would want to use this. First off, if you have endogomy in your family, meaning that you have lots of relatives that might have been third or fourth or fifth cousins that just intermarried over a long period of time, meaning you share a lot of the same DNA, and that means a lot of these segments might be just common throughout the entire population. In that case, you might want to change your segment size from seven to 10 or even 15, in which case now it’s going to eliminate any segments that are smaller than that. So hopefully what’s left is just gonna be the ones for those more closely related about three to five generations away from you. The other time that you might want to change the snip window is if you have kits that don’t share a lot of snips.

So if you watch that one to many video, there was some kits with overlap that only had about 50,000 snips. Now Genesis for the most part has adjusted for this, but what we can find is that if we put a smaller snip limit in and if we put a smaller segment size limit in, we’re gonna find more segments. The more likely it is when we share a lot of snips, then these segments are probably more just false matches or matches just because we’re from the same general population. So let me show you, I’m gonna actually change this snip threshold to 100 and I’m going to drop my minimum segment size down to four. Now you can see already on chromosome number one, there’s this five cento Morgans right at the beginning of that chromosome that was only 171 snips. So it falls below what that centre threshold is, and you can see here’s some other ones that are below that.

And so it’s finding some of these other segments that are much smaller. So if you’re going to use the snip threshold size, make sure you understand what it is useful for. Again, if you have a kit that you don’t share a lot of segments with, then it’s useful to change that snip size down to a lower level to hopefully find some more segments. But if you already share a lot of snips, if you’re over that a hundred thousand, then it’s probably not gonna be very useful cause it’s gonna find a lot of little segments that aren’t really matches. So this next one is called the mismatch bunching, and this is actually related to the snip size. It defaults by taking that snip size and dividing it by two. Let me show you what I mean by the mismatch bunching. So when the computer is looking at a match, it is looking to see that it has at least a half a match continuously for that time, but it allows for some mismatching.

You can see in this match right here, I have a half match over this 24 to 72 mega section of chromosome number three. It’s 51 centimorgan’s long, and it looks like there’s one little red mark right in the middle there, but it’s not been divided up into two segments. What that means is that the computer is going to look for the first mismatch and the first mismatch, it’s gonna basically create a marker. After that mismatch, it’s going to look to see how close the second mismatch is, and you can see in this case it’s not until the end here that that second mismatch is. If that mismatch is closer than half of the snip limit, the snip threshold that was that 200 to 400, then it’s going to cut it off and say that, hey, it’s no longer a match. And so in this case, there probably was not another one in the right range and that’s why it kept this all the way through.

And you can see that as you go down, there’s lots of different segments that might have one solitary one or sometimes even two solitary ones here on chromosome number 13, you can see a good example of where it found a first mismatch and then shortly thereafter it found a second mismatch and there likely was not. You know that 100 to 200 snips in between those two, and so it actually calls that a little no match in that area. Now if you change that bunching limit, it’s going to change whether or not it calls this a no match. So let’s see if we can actually change the values so that it is not a no match in that area, but it’s actually a match. So in order to do this, what I’m gonna do is I’m going to define my snip threshold and I’m gonna put my snip threshold at 500 and I’m going to make my bunching limit at 100.

And let’s go down to chromosome number 13 and we see, hey, at those levels it is still a mismatch. Let’s try to change that down to 50 now and there at 50 as a bunching limit. You can see those two red marks still show up, but it’s no longer called a no match in that section. So now this is calling the entire thing one great big section. Now, why do these mismatches happen? Sometimes those mismatches happen just in processing the DNA, and so they may be, they may be errors where it actually is called incorrectly. Sometimes it’s just because those are close together and there was different recombinations right in the same area. And so those really are multiple segments. Now that’s something that when you get more knowledgeable about how to analyze DNA that you may use these bunching limits and this snip window for probably most of your analysis.

You’re not going to use those. Now. The next one is to show fully matched segments, and this is those areas where you fully match people. So you really only want to use this when you know that you have siblings or double first cousins or something else where there’s going to be fully matched region because if I click on it right now, this is with me and my aunt, you’ll notice that there’s really no areas that we fully match, which is expected because she’s only related to me on one side of my family. But if I come back and I do this same thing now with my mom and her sister, then it’s going to highlight those areas that are fully matched areas, and so I can see, hey, what sections are fully matched. Now, they also will have half matches on some other areas, but this gives me the fully matched segments.

Now if you are doing some visual phasing, then this is a great tool to quickly be able to grab those numbers as far as where that fully matched region is. Now the last one is this prevent hard breaks. And this one might be a little bit difficult to understand, but it says that its default is to create a heartbreak when the distance between snips exceeds 500,000 base positions. Remember on your genome, the companies have analyzed about 700,000 positions. Some of these are more evenly spread out and in some cases they’re actually really far apart between one snip and the very next snip. And so what Genesis defaults to do is to create a hard break. So let me show you what this might mean. As we’re looking right here on chromosome number one, we can see that, hey, there is this segment right here that then it looks like there’s a part of it where it is a no match, and most likely this is because this has created a hard break.

There’s a snip, and then there’s about 500,000 bases before the next snip. And so it’s going to default and say, well, there’s a break there because it really doesn’t know whether or not it’s a match in that area. On the other hand, we can see overall with this green, the whole section before and after is a fully matched section. And so it’s really likely that that is fully matched in that section as well. If we go back and we click on this so that we prevent heartbreaks, so it doesn’t automatically put those in, we can see on chromosome number one, it has not broken up that segment. It has maintained that. Now as all one segment, and this is something that I do on almost every one of the searches on GEDmatch, is I don’t prevent those hard breaks. So when you’re doing a one to one comparison, one of the things I highly recommend is you actually go and change this so that this box is checked.

So that is how you can use the one to one match comparison, and it is a tool that you should actually use on all of your matches before you contact them because the one to many match is just a gross overall look at it. You wanna do the one to one comparison to make sure that you actually match on some segment of DNA and hopefully that that segment is significant enough and maybe you actually match some other family members on that same segment that you can be able to provide this match some information for. Now, if you have any questions about how to use the one to one comparison, put it in the comments below and I’ll try to answer it. And remember that X comparison is operates the exact same way. It’s just comparing the X chromosome. If you like this video, be sure to give it a thumbs up and share it with your friends.