How do you organize GEDmatch matches?

Question

I'm trying to find my "missing link" second great grandfather, which I've posted about in geneology help. I'm also interested in seeing which parts of my chromosomes come from which parts of my family. I've been trying to find, link, and sort DNA matches so I can hopefully find the "missing link" DNA as opposed to known family DNA or unknown how we match matches.

Does anyone have a good system for how they record a match when it's not strong enough to add to wikitree? Say a sixth cousin you need to triangulate to confirm, but haven't gotten the third match yet? Any tips or tricks are appreciated.
My best ideas right now are one or both of the following

* a massive spreadsheet of my family tree, with kit numbers and chromosomes they match under ancestor names, then a side list of unattached matches

* a "chromosome map" of each chromosome, with kit number and ancestor name indicated at the locations shared

These would both be rather messy and time consuming, but I don't want to lose an important match by not having some sort of way to record that I know a match there exists, and I'd prefer not to accidently re-email someone I forgot when we've already figured things out.

Answer 1

If you're referring to gedmatch.com, I use dnapainter (www.dnapainter.com) to map matches on individual chromosome pairs. You can add any information regarding your assumptions or beliefs to any match set.

Remember, match data is given for a chromosome PAIR. So, more importantly, if I believe the match is definitely paternal or maternal, I use dnapainter to map the match to the X or Y chromosome of the pair.

Then, should a third match to my results come along, I use gedmatch to compare the two DNA kits (other than myself). If those 2 provide a good match, you can assume, for the sake of argument, AND assuming there are not TWO unrelated ancestors among the 3 of you, you can map the new match to the paternal or maternal chromosome of any chromosome pair. That cuts in half the ancestors you need to research to find a possible connection to the new match.

dnapainter is convenient as you can cut-and-paste comparison results from gedmatch.com into a new entry on dnapainter.

EDIT: it takes a while to learn all the ins and outs of dnapainter, but it does allow editing of matches on a chromosome pair to an individual chromosome.

It's more convenient than a spreadsheet (which, like you, I used to do) as it not only provides digital information, but provides a graphical view of the mappings. It's nice to add a new match and see graphically (without comparing 7 digit numbers) that there is (or isn't) an overlap with other matches on a particular chromosome pair.

Comments

I had heard of DNA painter but I didn't know it let's you save matches? I thought it was more of a one and done comparison. That's exactly what I was looking for, thank you. I'll have to play with that this weekend.

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It's not at all a once-and-done. You can edit each match, or delete it. You can also create additional profiles, for yourself or another person.

I have a profile for matches for which I am highly confident, and another for "I have a match but haven't a CLUE what it means." I also have a couple profiles for some of my matches, to see if I can glean any information from THEIR matches.

You CAN download match information from dnapainter if you want to save it elsewhere, say, for reviewing off-line.

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Bruce Veazie, you lost me here: "Remember, match data is given for a chromosome PAIR. So, more importantly, if I believe the match is definitely paternal or maternal, I use dnapainter to map the match to the X or Y chromosome of the pair."

If I have a match with a segment on chromosome 9, for example, where does X or Y come in?

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I agree with Bruce. I've found dnapainter.com to be an excellent place to keep track of my auDNA matching information. And it's free!

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Not to put words in Bruce's mouth, but I believe he means "...use DNA Painter to map the match to either the paternal or maternal chromosome of the pair."  

Which may also be a cautionary advisory for DNA Painter. You can create multiple profiles, so you aren't constrained to one; and you can move stuff around. Early on, I just slammed everything I had onto one profile for myself. Mistake. The result was a whole bunch of segments that painted both the paternal and maternal chromosomes because I didn't yet know where those matches actually fit. I split things up so that my main, working profile contains only those matches where I absolutely know their inheritance path. The needs-work matches are in a different profile just waiting for enough information to be moved in with the "confident" neighbors.

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@Edison - yeah, I should've been more careful with regard to the order of the words - "paternal or maternal matches get matched to the Y or X [N.B. the order!] chromosome respectively." Good point. Luckily, dnapainter will match them appropriately if you select "Paternal" or "Maternal" relationship (rather than Unknown) for the match set.

@Thersa - determining whether a match on a chromosome pair is on the X or Y chromosome - there are a couple ways:

1. If you know the match is definitely on either the paternal side or the maternal side (from other information such as a family tree that you trust), then you can assign that match to the X (maternal side) or Y (paternal side) chromosome. Further, you can assign any other match with that person to the X or Y chromosome on the matched chromosome pair.

2. If you have already have another match (call it Match 1) on that chromosome pair which you have determined is on the X or Y chromosome, AND the new match (call it Match 2) overlaps the same region on the same chromosome pair, AND you check on gedcompare.com that the DNA kits for Match 1 and Match 2 are matches for each other, then Match 2 is on the same chromosome (X or Y) on any of your chromosome pairs.

Ex 1: You have a match with a cousin you know is on your father's side. You can assign all the matches with your cousin to the Y chromosome on any chromosome pair that gedcompare provides.

Ex 2: You have a match with an unknown person, and that match overlaps the same region (segment) with your (paternal) cousin. Then compare the unknown with your cousin on gedcompare. If they match, then you can assign any match with unknown to the Y chromosome on any chromosome pair.

In words, if unknown-someone matches you on chromosome 9 on a segment (say) from 9000-10000, AND your (paternal) cousin matches you on chromosome 9 from 9500-11000, AND your cousin and the unknown-person are a match, the unknown-someone is on the same side of your family as your cousin, and any of the chromosome pair matches with unknown-someone are on the Y chromosome.

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Thanks for clarifying - using X for maternal and Y for paternal caused the confusion.

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My sincerest apologies, Theresa. However, the Y chromosome in a pair IS the paternal chromosome. The X chromosome is maternal.

With regard to confirming a paternal or maternal relationsip, it should also be noted, the opposite is true:

In the example, if you have an overlapping segment with both an unknown and a paternal match, and through gedcompare you determine those 2 individuals are NOT related, then you can assign the unknown match to the maternal chromosome.

I'm lucky enough to have a maternal first cousin on gedcompare, and we have extensive matching sequences. I also have 2 occurrences of overlapping segments and my cousin has NO matches with those individuals. I've since determined that those 2 matches were, indeed, on my paternal side.

EDIT: Just a bit of info on how that can occur. DNA match data (by chromosome pair number and sequence locations) is generated AS IF the X and Y chromosomes are laid side-by-side. That is, a match at location 9000-10000 MAY come from the X chromosome OR the Y chromosome. So one cousin may match you at 9000-10000, and another cousin (unrelated to the the first cousin) may ALSO match you at 9000-10000. But one match comes from one chromosome of the pair and the other match comes from the other chromosome.

N.B., that DOESN'T mean that the two DNA sequences are the same; they're just on similar locations on the "side-by-side" chromosomes.

(Hah! THAT ought to confuse everyone!)

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Thanks for all the tips. I'm going to have a busy weekend! Hopefully I can get some matching magic going.

Answer 2

Allison,

I use a massive spreadsheet, I use DNA painter, and I use the the tier one tools at GEDMATCH - this allows me to see matches for a specific chromosome.

I find it interesting that I am also now finding some matches on MyHeritage - their DNA matching tools are useful and as they are tied to family trees they provide some clues.

None of this solves the problems - each provides a little bit.

Comments

I don't believe Philip intended to imply it, so just to clarify Philip's response - you don't need to use Tier One tools to see matches on specific chromosomes. The free version does that also.

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Bruce,

What I intended was that I can select a specific chromosome and look at matches ONLY for that chromosome using Tier One, I can not do that on the free version.  This is very useful when you have several thousand matches and wish to look at only one chromosome.

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Ah! I stand corrected. Your wording was correct.

Answer 3

GenomeMatePro is what I recommend to locate triangulated groups, track research, and map chromosomes. DNAPainter is an interesting 'visual after you have triangulated a segment for mapping.  GMP is free.  You can get it here:  https://www.getgmp.com/

Comments

I'm seconding the recommendation for Genome Mate Pro.

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Thanks, I've never heard of it.