PDA

View Full Version : Big Y



raspberry
12-21-2016, 07:54 PM
Hello, do you think that the "Big Y" test will be cheaper a few years later because of the progress of science. I have interest in doing a "Big Y" test, but I think the price is too high. So is it a good idea to wait or not? Who belongs to the older BigY tester generation and knows how the price changed?

Lugus
12-21-2016, 08:20 PM
Hello, do you think that the "Big Y" test will be cheaper a few years later because of the progress of science. I have interest in doing a "Big Y" test, but I think the price is too high. So is it a good idea to wait or not? Who belongs to the older BigY tester generation and knows how the price changed?

Someone said that it's hard to make predictions, especially about the future, but I believe prices will go down and I think they're already going down. With a voucher it's even cheaper.

If you're really excited about YDNA like me you won't be satisfied until you do a NGS test. That's why I think it's a waste of money to do SNP panels because anyway you'll end up doing a Big Y.

Oleg (Rus)
12-21-2016, 08:43 PM
I would wait and order Big Y only with a coupon. If even Big Y of FTDNA doesn't become cheaper, there will probably be another NGS tests in the market with better prices.

HansDB
12-21-2016, 08:52 PM
If you await the right moment you could combine a "Sales reduction" period with a reduction coupon (you also can use somebody else's coupon because they are transferable => try to find a 100$ coupon).
To maximize your BigY result you best upload them to YFull after the FTDNA analysis (this costs around $40). This way you'll get to know more SNP results and also around 200 STR results.
It is expensive, but you should see it in relation to the amount of hours you spend on this hobby (if you spend alot of time on it, it is worth the investment).

Lugus
12-21-2016, 08:52 PM
I would wait and order Big Y only with a coupon. If even Big Y of FTDNA doesn't become cheaper, there will probably be another NGS tests in the market with better prices.

I hope so. Competition is what really brings prices down. If NGS tests become cheaper more people will do them and we'll get a better understanding of the different subclades.

raspberry
12-21-2016, 09:29 PM
If you await the right moment you could combine a "Sales reduction" period with a reduction coupon (you also can use somebody else's coupon because they are transferable => try to find a 100$ coupon).
To maximize your BigY result you best upload them to YFull after the FTDNA analysis (this costs around $40). This way you'll get to know more SNP results and also around 200 STR results.
It is expensive, but you should see it in relation to the amount of hours you spend on this hobby (if you spend alot of time on it, it is worth the investment).

Yes, I also have coupons and holiday sale, but still I think it is too expensive and overprieced. And if you consider that y-dna 12 str markers costed around 1000$ at the beginning of this century, than it is very likely that the prices will fall (I googled it). I think if there would be scientists who are really interested in this subject this would be much cheaper (like y-seq, any Snp test for 14 euros while ftdna wants 39$). Also I will now write an E-mail to y-seq and ask if they think about doing such service (BigY). Also I doubt that this BigY test would be useful for me at the moment belonging to a basal clade of R1b wich is only added last year to the R1b tree.

Oleg (Rus)
12-21-2016, 09:34 PM
If you await the right moment you could combine a "Sales reduction" period with a reduction coupon (you also can use somebody else's coupon because they are transferable => try to find a 100$ coupon).
To maximize your BigY result you best upload them to YFull after the FTDNA analysis (this costs around $40). This way you'll get to know more SNP results and also around 200 STR results.
It is expensive, but you should see it in relation to the amount of hours you spend on this hobby (if you spend alot of time on it, it is worth the investment).

The will find more than 400 STRs, not around 200. And YFull worth it anyway, because it's the only way to find your specific place on the haplogroup tree.

lgmayka
12-21-2016, 10:13 PM
Also I doubt that this BigY test would be useful for me at the moment belonging to a basal clade of R1b wich is only added last year to the R1b tree.
The Big Y (and analysis) will get you onto YFull's haplotree. Then as soon as someone else in your clade does the same, YFull can estimate a TMRCA.

Take a look at this mysterious clade of Q (https://yfull.com/tree/Q-YP1669/), with only two known examples: one from Northern Ireland, the other from Lithuania. Their TMRCA is over 13,000 years! Does this mean that the clade has been in Europe that long? Maybe. (And maybe not, of course. :) )

Afshar
12-21-2016, 10:30 PM
I would not wait for it. Bringing the cost down depends on the acquirement of New machines which are very expensive. Maybe if the demand for BigY goes up then these steps will be taken.

Cofgene
12-22-2016, 12:04 AM
If you await the right moment you could combine a "Sales reduction" period with a reduction coupon (you also can use somebody else's coupon because they are transferable => try to find a 100$ coupon).
To maximize your BigY result you best upload them to YFull after the FTDNA analysis (this costs around $40). This way you'll get to know more SNP results and also around 200 STR results.
It is expensive, but you should see it in relation to the amount of hours you spend on this hobby (if you spend alot of time on it, it is worth the investment).


WRONG! Yfull will not identify more quality SNPs. They may find an additional one at a lower quality level but not at the high confirm able one. In reality you are looking at about 10% difference in the calls of the lower quality SNPs between FTDNA, YFull, and Full Genomes. A good % of the differences will end up in the not confirmed list when follow-up testing is performed. Yfull provides STR calls but that is questionable since they provide calls like DYS425=0 which is in reality an artifact of how Sanger sequencing works on that specific segment. YFulls provides a service to those haplogroups which never developed the technology to do their own analysis.

YFull's result seem to leave out MNPs and their tree has gaps due to it being limited only to SNPs.

Note that you can remove the FTDNA crap call variants just by comparing the "novel" variants list against the identified crap from the 780+ BigYs in the U106 project. Those results are available in the U106 Yahoo group file area.

lgmayka
12-22-2016, 01:57 AM
Yfull will not identify more quality SNPs.
YFull indeed finds reliable SNPs that FTDNA does not list. Perhaps more importantly, YFull verifies reliable SNPs that are expected but not found in FTDNA's list.


Yfull provides STR calls but that is questionable since they provide calls like DYS425=0 which is in reality an artifact of how Sanger sequencing works on that specific segment.
Yes, YFull's Y-STR calls generally try to be compatible with FTDNA's.


YFulls provides a service to those haplogroups which never developed the technology to do their own analysis.
You are correct that those lucky few who fall into the most popular portions of the most popular haplogroup can avail themselves of a free third-party service roughly comparable to that of YFull. Even for the lucky few, though, YFull offers the advantage of a haplotree that meets academic criteria, a personal account with a searchable database of results, TMRCAs, etc. Why not submit one's results to both?

Celt_??
12-22-2016, 02:32 AM
I purchased the Y- Full with the $50 Holiday discount and a $75 coupon = $125 off the full price of $575. I paid $450. My results showed that I have 38 Novel Variants or unique mutations which are not yet officially recognized and haven't been given a name. Therefore, my Haplogroup remained the same as it was after SNP Pack testing: R - CTS9733. As mentioned above, over time some of my Novel Variants will be recognized, given names and then my terminal SNP will change.

I uploaded my data to Alex Williamson at The Big Y and my results are shown in attached chart below ( my results are surrounded by red ). They are in red because Alex hasn't finalized his analysis - and because my Novel Variants haven't been recognized. I, like many people, must wait until more folks are tested to learn more.

13240

My impression is that if a person has his full Y chromosome sequenced this issue is vastly greater - many, many more Novel Variants which are not recognized and not named. But a full Y sequence will never have to be done again although one must pay to have it re-analyzed each time ISSOG updates its phylogenetic tree i. e. adds newly recognized SNPs and branches.

CONCLUSIONS:
1) If you are current on FTDNA SNP Pack testing, you won't learn much immediately from Big Y as I didn't, so why not wait?

2) If you have only done Single Tandem Repeat (STR) testing (Y-37, Y-64 or Y-111) and only have a provisional Haplogroup like R - M269, then a good argument can be made for jumping to the Big Y test now at $450 rather than doing 2 or 3 SNP Packs

- IF YOU ARE SERIOUSLY INTERESTED IN GENETIC GENEALOGY.

FrankAlbion
12-22-2016, 02:59 AM
Were either Mr Leal (apparently with Portuguese ancestry) or Mr Lundin (apparently with Swedish ancestry) able to provide useful hints? Both are CTS9733 per your Big Tree figure.

lgmayka
12-22-2016, 03:23 AM
But a full Y sequence will never have to be done again although one must pay to have it analyzed again each time ISSOG updates their phylogenetic tree i. e. adds newly recognized SNPs.
Who charges for re-analysis? Certainly not YFull. YFull's analysis is essentially continual (i.e., with each new revision of their tree) for a one-time fee.

You actually mentioned Alex's analysis. His service is free.

Celt_??
12-22-2016, 06:21 AM
DUPLICATE

Celt_??
12-22-2016, 06:33 AM
Who charges for re-analysis? Certainly not YFull. YFull's analysis is essentially continual (i.e., with each new revision of their tree) for a one-time fee.

You actually mentioned Alex's analysis. His service is free.


FGC Corp (which performs Y-DNA sequencing i.e. Y-Elite) charges $25 to have one's data re-analyzed after each update, if you want it done. See this thread and page 163: http://www.anthrogenica.com/showthre...-Pilot/page163

"Are the current Y-Elite analyses converted to build 38 reference from build 37? If so is it possible to get previous build 37 versions of Y-Elite results reanalyzed to the build 38 reference? Thanks"

FGC Corp: "The build 38 analysis is a separate analysis. So, yes, the $25 Build 38 analysis is an additional step."
----------------------------

Alex Williamson doesn't perform Y-DNA sequencing so, of course, I wasn't speaking of him.

Celt_??
12-22-2016, 06:44 AM
Were either Mr Leal (apparently with Portuguese ancestry) or Mr Lundin (apparently with Swedish ancestry) able to provide useful hints? Both are CTS9733 per your Big Tree figure.

The Time to Most Recent Common Ancestor for CTS9733 is 3900 years before present - that's ~1900 BC, during the Bronze Age. I have considered emailing them but what should I ask Mr. Leal and Mr. Lundin?

"Do you know the name of our MRCA or his wife's name? Maybe their childrens' names and birth dates?" ;)

No, seriously, two weeks ago I did email one of my FTDNA Big Y "matches", a PhD in Sweden, and have received no reply. My suspicion is that he found my question dumb considering the TMRCA.

Celt_??
12-22-2016, 06:50 AM
[QUOTE=

JamesKane
12-22-2016, 10:49 AM
FGC Corp (which performs Y-DNA sequencing i.e. Y-Elite) charges $25 to have one's data re-analyzed after each update, if you want it done. See this thread and page 163: http://www.anthrogenica.com/showthre...-Pilot/page163


Right, this fee is to redo the entire analysis using the latest human genome reference build. It has nothing to do with the state of ISOGG's tree.

The big changes in using GRCh38:
1) The centromere sequence has been added.
2) Several mistakes for positioning were fixed. Small segments of chromosomes 1 through 10 are now on Y and some segments that were on Y have moved to X.
3) A range of DYZ19 was separated into chrY_KI270740v1_random. This is because the 37,240 bases cannot be firmly fixed for position.

An NGS tester doesn't need to do this, but some new branch markers can be identified this way. My experimental tree for R-FGC11134 is entirely based on the new reference. http://www.haplogroup-r.org/tree/R-FGC11134.html

Celt_??
12-22-2016, 01:52 PM
My experimental tree for R-FGC11134 is entirely based on the new reference. http://www.haplogroup-r.org/tree/R-FGC11134.html

Your tree is very detailed and impressive. Is there a way for me to access a similar L-20 tree at http://www.haplogroup-r.org . Thank you

FrankAlbion
12-22-2016, 02:02 PM
I'll try a direct email late today and copy you.

JamesKane
12-23-2016, 01:30 AM
Your tree is very detailed and impressive. Is there a way for me to access a similar L-20 tree at http://www.haplogroup-r.org . Thank you

The R-FGC11134 branch is really the only well developed section. I have access to virtually all of the original BAMs for that part of the tree.

The R-L20 branch is currently shown on the main tree (and another sub-tree at http://www.haplogroup-r.org/tree/R-P312.html.) While I have a good number the FTDNA VCFs of the Big Ys on the branch it would be a duplicative effort to establish the branching structure to Alex's work using them. As more of the U152 folks supply a BAM (or the b38 analysis from FGC) I'll revisit those sections.

TigerMW
12-23-2016, 12:28 PM
I want to make sure everyone knows.

FTDNA provides a BAM file interpretation and comparison across their whole database when you place a request to Michael Sager (on their Y team) for a haplotree update. This is free and is similar to what other interpretation services do but there are no reports provided, just an email response with what he found.

There are still $100 discount coupons popping up. I received several yesterday and am posting these particular ones on the R1b project activity feed (because that was part of the deal of getting the coupons.)
https://www.familytreedna.com/groups/r-1b/activity-feed

JMcB
12-23-2016, 03:02 PM
I want to make sure everyone knows.

FTDNA provides a BAM file interpretation and comparison across their whole database when you place a request to Michael Sager (on their Y team) for a haplotree update. This is free and is similar to what other interpretation services do but there are no reports provided, just an email response with what he found.

There are still $100 discount coupons popping up. I received several yesterday and am posting these particular ones on the R1b project activity feed (because that was part of the deal of getting the coupons.)
https://www.familytreedna.com/groups/r-1b/activity-feed

Hello Mike,

How would one go about doing that; that is, contacting Michael Sager and asking for a haplotree update. Especially in a case like mine where they seem to have already updated the haplotree by splitting me off from I-L234. Which is were YFull has me because they don't yet know that I'm positive for 9 of L234's defining SNPs but negative for L234.

vettor
12-23-2016, 04:22 PM
I want to make sure everyone knows.

FTDNA provides a BAM file interpretation and comparison across their whole database when you place a request to Michael Sager (on their Y team) for a haplotree update. This is free and is similar to what other interpretation services do but there are no reports provided, just an email response with what he found.

There are still $100 discount coupons popping up. I received several yesterday and am posting these particular ones on the R1b project activity feed (because that was part of the deal of getting the coupons.)
https://www.familytreedna.com/groups/r-1b/activity-feed

Who initiates this BAM file interpretation ? ............Michael Sager, or do we need to ask ?

Would not the ftdna project that one belongs to take the initiative to realise a member has done the BigY and that important data can come from it

lgmayka
12-24-2016, 02:16 AM
FTDNA provides a BAM file interpretation and comparison across their whole database when you place a request to Michael Sager (on their Y team) for a haplotree update. This is free and is similar to what other interpretation services do but there are no reports provided, just an email response with what he found.
How does one contact him, and exactly what do you get? I can imagine him sending you a list of reliable unshared SNPs (i.e., SNPs unique to yourself). What else? Is he permitted to tell you that "you share these 3 reliable SNPs with John Doe and no one else, so you two form a clade"? Does he tell you that "you tested positive for 2 of the SNPs at that level, but negative for the third, so we have to split that level"?

And of course, the obvious question: If FTDNA is willing to do this for any of their customers for free, they why don't they just do it automatically for everyone? Why do they wait until someone in-the-know sends an explicit request to a double-dog-secret contact?

JMcB
12-24-2016, 03:52 AM
I would imagine that it's probably just a courtesy that's preformed by Michael Sagar and if it was more generally known, he would soon be overwhelmed. But I'm guessing. My question is this, why hasn't FTDNA offered an interpretation service like YFull's or FGC's? I sure people would gladly pay the price and would prefer keeping it in house instead of having to send their Bam files here and there. Not that it's all that difficult but still.

JamesKane
12-24-2016, 01:21 PM
How does one contact him, and exactly what do you get? I can imagine him sending you a list of reliable unshared SNPs (i.e., SNPs unique to yourself). What else? Is he permitted to tell you that "you share these 3 reliable SNPs with John Doe and no one else, so you two form a clade"? Does he tell you that "you tested positive for 2 of the SNPs at that level, but negative for the third, so we have to split that level"?

Michael is the contact for getting FTDNA's tree updated. You send him the proposed branch and kits who have tested at FTDNA who support the placement. I don't believe he is interested in checking your singletons. That is a totally self-serviceable task with your BAM and a viewer like IGV.

When he makes the updates, he tends to look at the surrounding region and add branches he sees at the time.

lgmayka
12-26-2016, 09:41 PM
Michael is the contact for getting FTDNA's tree updated. You send him the proposed branch and kits who have tested at FTDNA who support the placement. I don't believe he is interested in checking your singletons. That is a totally self-serviceable task with your BAM and a viewer like IGV.
That's certainly very useful (if anyone can figure out how to get a hold of him), but it's totally different from what Mikewww wrote a few posts earlier.