Big Y, what next?

General discussions regarding DNA and its uses in genealogy research

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Mon Jan 30, 2017 6:31 am
When a tester gets his Big Y results he should consider sending his BAM file to Yfull and also to ask his match to do the same. A tester will get at least 400 YSTRs and some YSNPs that are not in the VCF file. One will also get an estimated TMRCA for their branch. I have 46 SNPs with only 2 reads which is below the threshold that FTDNA uses, but that does not mean that the SNPs are not valid.
The Big Y gave me 32 good quality SNPs to work with and 10 of them occurred within the last 1,250.

When I got my Big Y results I downloaded the VCF file and opened it in excel.
I extracted all the YSNPs that are marker passed, example, chrY 9374685 . G C 133.073 PASS . GT 1. I had around 200 and I looked the positions up in the Ybrowse site to see if they were already named YSNPs. Since I had my BAM file analyzed by Yfull I can use the "browse raw data" feature.


Every Big Y tester should send his novel SNP list to Michael Sager at FTDNA so that he can add them to the FTDNA tree if he has not already done so. He will need two testers with the same SNPs. He does not add singletons to the tree and nor does YFull.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu Feb 09, 2017 8:46 am
Gioiello
We need to encourage as many testers as possible to take the Big Y test because FTDNA has 580,000 Y testers on their books. It is also the most reasonable NGS test for the price. The Big Y test should be sufficient enough for most people to connect to their paper trail. I have 10 quality SNPs within the last 1,250 years and my match has the same number also. I have some indels and lots of YSTR's to work as well. I know that you have an issue with no-calls but there are ways around that. All of the testers are clever enough to sort out their own YSNPs from the Big Y. All they need is a little bit of tuition and co-operation from their matches.

Posts: 2409
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
R- Z2110 (KV7Y2)
MtDNA:
K1a1b1e/HQ176413
PostPosted: Thu Feb 09, 2017 12:24 pm
dartraighe wrote:Gioiello
We need to encourage as many testers as possible to take the Big Y test because FTDNA has 580,000 Y testers on their books. It is also the most reasonable NGS test for the price. The Big Y test should be sufficient enough for most people to connect to their paper trail. I have 10 quality SNPs within the last 1,250 years and my match has the same number also. I have some indels and lots of YSTR's to work as well. I know that you have an issue with no-calls but there are ways around that. All of the testers are clever enough to sort out their own YSNPs from the Big Y. All they need is a little bit of tuition and co-operation from their matches.


Not only I have problems with Big Y (which is around 15200 no calls now out of about 100,000 SNPs as to YFull), and the problem is above all for who have only some old SNPs in common and it risks not being catched, the worst is for me the "criminal firm" with its agendas, its wrong tests, its useles SNPs (they always have PF6714 even though I wrote many times that it isn't downstream L11 but a SNPs in the hg. R-U152 found in Sardinians with a long deletion). No prisoners.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu Feb 09, 2017 1:58 pm
Gioiello wrote:
dartraighe wrote:Gioiello
We need to encourage as many testers as possible to take the Big Y test because FTDNA has 580,000 Y testers on their books. It is also the most reasonable NGS test for the price. The Big Y test should be sufficient enough for most people to connect to their paper trail. I have 10 quality SNPs within the last 1,250 years and my match has the same number also. I have some indels and lots of YSTR's to work as well. I know that you have an issue with no-calls but there are ways around that. All of the testers are clever enough to sort out their own YSNPs from the Big Y. All they need is a little bit of tuition and co-operation from their matches.


Not only I have problems with Big Y (which is around 15200 no calls now out of about 100,000 SNPs as to YFull), and the problem is above all for who have only some old SNPs in common and it risks not being catched, the worst is for me the "criminal firm" with its agendas, its wrong tests, its useles SNPs (they always have PF6714 even though I wrote many times that it isn't downstream L11 but a SNPs in the hg. R-U152 found in Sardinians with a long deletion). No prisoners.



I disagree, the Big Y has been for me the best test that I have taken so far. I don't have any concerns about no-calls. They will get all those things right some time in the future. FGC is too expensive for the majority of testers. There is no other company out there with a huge database like FTDNA that does YDNA tests. The U106 group has made huge progress with more than 848 Big Y tests and they are out in front of any other YDNA group at present.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Mon Mar 06, 2017 10:36 am
After the Big Y most testers will end up with a block of novel variant YSNPs. If one cannot break down the SNP block into divergent branches then it is possible that there was a bottleneck in their most recent ancestral line. Bottlenecks are bad news for any researcher because one cannot hope to find the origin pathway of their specific Y line. We can see that M222 went through a bottleneck until 2,000 ybp and then expanded in north west Ireland and Scotland. We can only assume that the M222 bottleneck happened somewhere in that region were most descendants come from today. Will ancient dna help us to solve it?!!!!!!!!!!!

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu Mar 23, 2017 12:56 pm
My view on SNP packs is, do not waste money on them. During an FTDNA sale one can buy a Big Y test for 450 dollars if one already has taken a 12 marker YDNA test. With an SNP pack it is possible that one will only test positive for one of the SNPs in the pack and with Big Y one should get all the SNPs that they need to match with their paper trail. Furthermore, the SNPs packs are designed by the project admins and they have a say which SNPs go in and which do not. If a tester wants to make progress in their own specific line then the Big Y is the most economical test at present and should be sufficient.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Mon Apr 24, 2017 5:19 pm
I have my son's BAM file results from Yfull and we have the exact same number of YSNPs under Z156, 25 shared with another Irish origin tester and 9 private/family YSNPs. I await the YSTR results. Also, I have a lot of recurrent SNPs under Z156 which may come in useful at some time in the future. The Big Y test is accurate and the nine private/family SNPs happened within the last 1,250 years according to Yfull's TMRCA for my branch. The two Big Y tests have confirmed the quality of our YSNPs and I am still learning.
Last edited by dartraighe on Wed May 17, 2017 8:21 pm, edited 1 time in total.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Mon May 01, 2017 12:20 pm
Dr Iain answers to a few queries.

"> 1. I have a brother and paternal cousin in FTdna's system. Do I have to do a Big Y on one of them to get the age estimation? If yes which one?
Neither of these would be particularly useful. What I provide ages for are the relationships between testers. So testing your brother would give you the age of your father. Testing your first cousin would give you the age of your grandfather. You need much, much older relations to provide useful tests.

> 2. I know the both match me at Y-12. How far out should I test them? Y25, 37, 67 or 111? Will this be useful for the group and I?
Brothers and first cousins should match almost exactly out to Y-111 and on BigY. There's very little point in testing them with Y-DNA tests.

> 3. If I do a Big Y on one of them or both will FTdna's system pick up on their novel and possibly form a new clade than BY16584?
There is only a small chance (25-50%) that either one of them will have a novel variant compared to you. This would technically form a new clade, but it wouldn't be a useful one. It may identify some SNPs that were not called in your test, but you'd be better off taking a higher-resolution test if you have an interest in those (e.g. YElite or WGS at Full Genomes Corp.)."

Posts: 2409
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
R- Z2110 (KV7Y2)
MtDNA:
K1a1b1e/HQ176413
PostPosted: Mon May 01, 2017 1:04 pm
" It may identify some SNPs that were not called in your test, but you'd be better off taking a higher-resolution test if you have an interest in those (e.g. YElite or WGS at Full Genomes Corp.)"

I agree with him.

Posts: 2231
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Wed May 17, 2017 8:32 pm
There is no need to Big Y test sons, brothers, first cousins etc. One test will cover a lot of relatives but it is important to produce a good dna sample. Yfull will do a good job on the analysis.

I would like FTDNA to have SNP panels available to test similar to YSEQ. A lot of testers end up with 30-40 singletons after a Big Y test but these singleton SNPs are not for sale at FTDNA. The SNP packs are not good enough. None of my singleton SNPs are included in any of the SNP packs so I can't make any progress. I have to wait until someone takes a Big Y test and just happens to match some of my singleton SNPs.

There is no way that all of my 34 YSNPs from my Big Y test will be made available in any SNP pack. If anyone has 67 markers tested look in ysearch to see if you have any matches within a GD of ten @ 67 markers. One of your matches may have YSNP tested already. It is possible that one could pay 119$ for only one SNP within the SNP pack. A Big Y or YElite test is the best way to go if one wants to find all the YDNA mutations in their own specific line.
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