How do I isolate DNA matches on my dad's paternal side from my tests?

+11 votes
1.2k views
My dad passed away before identifying his biological father.  His biological mother has also passed away, but her identity is known and as been confirmed through documentation and multiple DNA matches.

I have had multiple family members tested and I am trying to isolate potential matches on my father's paternal side by process of elimination. Without a Y test, what is the best way to determine what DNA came from my dad?

I've tested the following and have uploaded all to GEDMATCH:

My Mother

Myself

My Half-Brother (shared Father)

My Half-Sister (shared Mother)

My son from first marriage

My son and daughter from second marriage

Thank you!
in Genealogy Help by Heather Collier G2G Crew (630 points)

4 Answers

+17 votes
 
Best answer

Hi, Heather. Since you and your mother are both tested and have kits at GEDmatch, the quickest solution is to use GEDmatch's phasing tool, available in the standard toolset:

All you need to do is select your mother's kit number and your own, and GEDmatch will generate two new kits for you, kits that will approximate, using mathematical algorithms, "pseudo-genomes" for each parent. Of course, you don't need you mother's, but the new kit named PxxxxP1 will represent your father and will remain on file for you to use.

The caveats: It won't show up on one-to-many matches run by others, so it won't be in the general "pool" like your own information. But you can use the kit just like any standard kit for one-to-one, one-or-both, and other comparisons.

Second, algorithmic phasing isn't perfect. Greatly simplified, what it's doing is looking at your mom's DNA and at your DNA, and assuming that whatever you have that didn't come from your mom came from your dad. Not perfect, but still a big help. In my experience, matches against the phased kit generally look about a half-step farther removed than they really are. But what it will give you is a tool to use to evaluate cousin matches against your father's virtual kit. If a cousin matches the new pseudo-genome and doesn't match your mother, you can be assured the DNA sharing is from your father's side of the family.

Happy hunting!

by Edison Williams G2G6 Pilot (248k points)
selected by Maggie N.
Thank you!  I had done the phasing like that before, but wasn't sure where to go from there and how accurate it would be, so your answer gives me new hope to try it again with direction!

Is there any phasing tool that would also consider the other DNA test relationships I have to further define the phased results?  I was thinking that because my half brother and I share our dad, that it could first eliminate my mom's DNA, then look at what my brother and I share, what my brother shares with my kids, etc... But the phasing tool only has parent/child.  

Could I further exclude any X-matches?  Any X-matches should not be from my father's paternal line, right?

Thank you again so much!  I have spreadsheet after spreadsheet and I'd like to be confident that I'm understanding the correct way to narrow down the matches so I can get closer to what I'm looking for.

:)

There is another phasing tool you can use if you have other known relatives of your father you can bring into play; your own children and half-siblings won't really help here. It's a GEDmatch Tier 1 tool, meaning you'll need to pay for at least month month of service in order to use it, but it's cheap.

Once you're logged into GEDmatch, you can use this link to read about the Lazarus utility: https://www.gedmatch.com/gedwiki/index.php?title=Lazarus. It's a bit more complex than the simple parent phasing tool, but offers more flexibility--and potentially greater accuracy--because of it. With the right combination of relatives' test kits, it can even be used to synthesize "pseudo-genomes" for long-passed grandparents. But it requires advance planning in the form of preparing a list of the kits on GEDmatch you want to use.

There are three places kit numbers will be entered. The first is optional but, similar to the regular phasing tool, brings your mother into the evaluation, which helps. The spouse's kit entered here must be the parent or grandparent of all the direct descendants in Group 1. And that's exactly what Group 1 is: direct descendants of both your father and mother (if you enter your mother's kit). You can enter up to 10 kit numbers here; this is where you'll put your own kit number. Your three children could go here, but there's no advantage to it, and GEDmatch recommends using only the closest direct descendants (if you had a full sibling, you'd use him or her, as well).

Group 2 is the trickier one. You can enter up to an overwhelming 100 kit numbers here. It looks like overkill, but the more the merrier if you have no close relations to your father to use. Group 2 is for relatives--but not descendants--of your father, the target of the pseudo-kit. Generally in order of best-to-use: parents (which I've never yet seen available for a Lazarus run, but there it is); full siblings (your aunts or uncles); aunts/uncles or nieces/nephews of your father; and then cousins in descending order of closeness. The key here is that the people entered in Group 2 should have no biological relationship to you mother. If you aren't solidly convinced that a cousin of yours is not strictly from your father's side, don't use him. Mixing in maternal cousins will foul-up the resulting pseudo-kit.

In the segment threshold settings, if you've been able to use one of your father's siblings, aunts/uncles, or a couple of 1st cousins, I'd choose "7.5 cM 50% Real Matches." If you're only able to add cousins, I'd stick with the default "6.5 cM 25% Real Matches." If you start at 7.5 and the trial run doesn't provide at least 1,500 cM in the resulting kit, you can drop it to 6.5.

The processing options offer a trial run, no batch processing, and full processing. Do a trial run first. You're shooting for a kit that contains at least 1,500 cM in shared segments; that enables the kit to go through full batch processing so that it's available to use for one-to-many and other multi-kit comparisons. Less, you can still generate a kit but you can use it only in one-to-one comparisons.

The final caveat from GEDmatch my cause your head to tilt: "the resulting surrogate kit does not contain any SNPs for segments where there was no reference data." Hmm...

Since GEDmatch uses raw data from different test providers, they're actually comparing oranges and tangerines: the various test providers don't all record the same SNPs. For example, 23andMe tests using the new v5 GSA chip can't be used in the regular GEDmatch at all because the SNPs tested don't align with the older Omni chip and the results from the other testing companies (yet; they're all going to have to go the GSA chip). Ancestry v2 results provided about 650,000 SNPs when uploaded to GEDmatch; 23andMe v3 tests had about 640,000 SNPs that could be compared to Ancestry's; and 23andMe v4 tests about 300,000 SNPs. So it's only a true oranges-to-oranges if you're looking at two kits tested at the same company under the same chip version. That's what GEDmatch means with that cryptic sentence. If, for example, you're working with one kit from AncestryDNA v2 and one from 23andMe v4, there are only about 300,000 in play because the others tested aren't in the same locations. Lowest common denominator. For phasing, including Lazarus, the new pseudo-kit can contain only information about the SNPs that could serve as reference data. But don't let the mumbo jumbo scare you off trying Lazarus. It's just something to keep in mind if you can't hit that 1,500 cM threshold.

 

I can't thank you enough for your answer - this helps explain all the areas I have been unsure about as I have made my way around GEDMatch.  I gladly pay the $10 for the Tier 1 - I just never have really known the correct way to use some of the Tier 1 tools for my specific search.  Your explanation makes total sense to me now so I'll give it a whirl. ;)

For the Lazarus, I have confirmed many DNA matches on my father's mother's side - will this still work since I'm interested in identifying matches on the paternal side?
This is awesome to know! I've been planning to do this! I've tested at least 15 of my relatives (both sides). Both of my parent's are gone and so is my only sibling. Hoping to one day create kits for them. I will go for grandparents for now though when I get more kit results back. Thanks again!
for me the best way to determine which relatives come from my mons side or my dads side is look at the surnames your dna relatives post. I can tell which side they are from that way
+13 votes
Another useful function on gedmatch would be to look at people who match both of two kits. You will get useful information from this if you run it for you and your half-brother and then for you and your half-sister. The matches in each case will be for the relevant side of the family.
by Lynda Crackett G2G6 Pilot (627k points)
Thank you!  I've done this too, but then didn't know how to separate the paternal from the maternal matches for our shared matches on my father's side.  I was hoping to use the X matches somehow to further eliminate the maternal side.  I want to end up with only paternal matches on my father's side to try to figure out his biological father's line.

:)
You cannot use the X matches in that way. A matching X would tell you that it could not be on your father’s paternal line as it cannot go through two consecutive males. Absence of an X-match could just be a result of two males further up the tree or could just be that they did not inherit the same segments of X, so you cannot draw any particular conclusion from its absence.
Thank you!  I was hoping to use the X-match to just trim away those matches that absolutely could not be from his paternal side, because his maternal side has tons of matches.  Understandably the resulting matches could not produce the list I'm looking for, but at least make it a little easier to navigate.  Would that work the way I'm thinking it could?

Again, thank you so much for your responses! :)
A positive X-match can help you to identify and trim any line that goes through two consecutive males. A non-match on the X should not be used alone to deduce which side.
+4 votes
Heather

If your goal is see which of your own matches are paternal then, as Edison has already pointed out, the phasing tool at gedmatch will do this for you.

If you want to take this a little further and try to do a larger reconstruction of your father's profile then you need to have more data than you have at present.

Your phased data represents 50% of your father's DNA.

If you are able to test your half-brother's mother, then you can phase his data, which will also give you 50% of your joint father's DNA. Only the bits where you do not match your half brother's phased results add to the picture - likely to be around another 25%.

Every paternal first cousin that you can add will help complete the picture.

I'm currently working on an improved version of the gedmatch Lazarus tool which does not go far enough in my opinion. I have three full siblings and four first cousins in the pool of data. My best estimate is that with this sample set I can get just about all of one strand and about 70% of the second strand for each of my parents.

You've got a head start on me with your mother-daughter set, but you really need some cousins to add to the mix.
by Derrick Watson G2G6 Mach 3 (31.8k points)
I could kick myself for not posting sooner!  You guys are really knowledgeable and so helpful!

I also have 2 half-sisters from my dad, and my stepmom, but I just haven't had them tested yet.  I'll work on that next - the turnaround time with Ancestry was phenomenal this last set I did!  I ordered them on 9/22 and had results on 10/18, so hopefully I won't have to wait long for this info.

I'll gather his first cousin matches in the meantime and hopefully make some ground.

Thanks again for being so helpful!
0 votes
My matches automatically sort in FTDNA from linking my matches to my family tree I created in there. I love it!! My dad's side gets blue boys and my mom's side gets pink girls. I've tested ppl on both sides of my family. GEDmatch is a great way to do it too! Try both!
by Debbie Parsons G2G6 Pilot (138k points)

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