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-- When Will you Include SNP Testers without Big-Y?
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Hi James—? Great work you are doing, but some of us don't need to pay for Big-Y since we leapfrogged directly to SNP panels.? That is my case, I have a Y-Seq test that takes me down to A6507, possibly revising to A6506 as testing progresses.? Either way it
traces to Castletown Beara, so I'm firmly CTS4166 and would like to show as that so others can find me.? ?
Do you have any plans to move beyond STR to SNP.? Isn't that the more precise method in any case, since STR seem to bounce around quite a bit in subclades?? ?Also, what about Autosomal, which has yielded many great results for me on Ancestry, with 4 separate
populations of cousins from 4 grandparents.
In any case,? happy new year from Santa Fe, NM.? Please include my MSN address copied here in any response, as the email I use daily unlike Gmail.? ?
Regards,
Mark E. Dunham (Bio-Sullivan)
Organizer & Volunteer
505-795-0199
From: [email protected] <[email protected]> on behalf of James Kane via groups.io <jkane@...>
Sent: Wednesday, January 1, 2025 9:01 PM To: [email protected] <[email protected]> Subject: [R1b-CTS4466-Plus] R1b-CTS4466+ BAM Tracker Updated ?
I've added a 'Tree-Premilinary-Pass' tab to this sheet and will be making some updates over the next couple days, but if you're interested in an "uncooked" version of the Joint Genotyping results you can find them there. ?There are about 100 non-FGC11134 men in here that are acting as an outgroup and preventing some oddities in Big Y from clustering away from the normal WGS results. ?
If Column A does not start with R1b and Column F doesn't have a name, it's potentially a new branch unique to hs1's coordinates.
The sheet will be updated with the FTDNA kit#s and regrouped by their subclade probably this weekend unless I see a need to go back and rerun the tree inference again. ?Anything that the A0-T man, HG02984, is derived for will be tossed in the end. ?
Otherwise, it looks like the age of some subclades is going to get pushed back with more equivalent SNPs.
?
Any questions or concerns, feel free to reach out.
James |
Mark, Food for thought. Just so you're aware, you didn't "leapfrog" BigY. SNP Panels have limited use and only can identify?based on previous BIgY testers to the point where you don't share a common ancestor. They will never replace?BigY nor are they better. R-A6507 branches off over 1,300 years ago (which is well before the advent of surnames). You will never be able to come down your line on the backs of other testers..you will always need BigY or equivalent Discovery Test to actually identify?YOUR?line of SNP mutations and build new branches. Testing individual downstream SNPs is not generally useful or productive, and just?takes time and extra money. It isn't a recommended way to understand your own place on the tree. The best way is to do a BIgY, see how far down the tree you get, recruit Y STR matches?to upgrade as well, until you've got a fairly recent branch on the tree (within the last few hundred years). Autosomal DNA is only useful overall within the last several generations, and sometimes not even then when endogamy is involved. Most Y DNA matches don't share ANY autosomal DNA so it is not in the realm of haplotree creation. They are two very different?things. Autosomal DNA use for this endeavour is biologically limited since it isn't connected to SNP data nor can you ascertain patrilines from it. As for STRs, James doesn't?use them in isolation. The STR values (including the extended panels of STRs from BIgY testing) are examined?and applied to an already mapped of haplotree using BIgY SNPs. Panel SNPs can't really be used that well because it leaves ambiguity since you've stopped short of where you should?be and you don't have any extended?BigY STRs to add to the project/tree. STR patterns can be noticed when dealing with large numbers of men over a wide timeframe, especially?those which have a consistent pattern across multiple branches. Those STRs which are more unstable aren't easily used. BUt STRs alone are never used in modern day genetic genealogy and haplotree creation. Hope that helps. Lucas McCaw, BSc., BEd. On Fri, Jan 3, 2025 at 1:29?PM Mark-dSF (Bio-Sullivan) via <medunham2=[email protected]> wrote:
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I'm pretty much in full concurrence with Lucas. ?At the risk of offending some, I will go further with STRs and say they are most useful for matching dead people or newcomers who receive outdated testing advice. ?Everyone else has moved on to either targeted capture or even whole genome sequencing now that the cost is under $400. ?Long reads are where the cutting edge is and are very difficult to find a lab doing direct-2-consumer for these at an affordable price. ?I really think a 10-15x PacBio HiFi WGS would be the optimum next step. ?No-one offers it yet, perhaps I need to find a couple million for a startup. ?:D
?
When you have a SNP signature fully resolved to modern era, then STRs can be used to eke out a few more possible branches in the region. ?That's why I exposed the STR charts that extend all the way through what Big Y currently offers.
As far as including SNPs in my analysis, they are already integrated into the tree. ?I believe you are this last kit in the branch here: ?
There are two branches under CTS4466 which are defined by members taking their list of private SNPs from a Big Y and testing only those in a close relative. ?This requires that you have been fortunate enough to be able to winnow the list down by using your other matches though.
From the investigator SNP Report in the R1b-CTS4466 Plus warehouse project, it looks like you have one of the ten SNPs in the current block tested. ?So the strategy would be test the private variants in the two men who defined the block to see if you are closer to one of them, and then fall back to the other 9 equivalents should you fail to have success in the other tests. ?The worst case expense is equivalent to a 30x WGS from YSEQ. ?I understand that this is a large investment that not everyone can manage, but expect the prices to continue to come down as the companies making the sequencers continue to improve the cost of doing the tests. ?
Any ways... welcome to the wild world of genetic genealogy. ?You can invest as much or as little as you can afford and try to learn more about your ancestor's origins using many different approaches. James Kane |
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