Big Y upgrade

General discussions regarding DNA and its uses in genealogy research

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Wed Dec 27, 2017 9:26 pm
Some posters on the FTDNA forum complain about the lack of matches after a Big Y test. I don't believe it is the fault of FTDNA. If one belongs to a rare dna group they will find it hard to find matches despite the fact that 1000's of people are taking tests. I belong to a rare branch with just one close match in eleven years.

There are a lot of testers at FTDNA who are not willing to go beyond 12 and 25 YSTR markers and a lot more who seem to have no interest in YSNP tests. There is not a lot that we the most advanced testers and FTDNA can do about that.

I sent in 20 named SNPs to FTDNA that are not in the FTDNA Y tree. They are new to me and came from the Big Y Hg38 upgrade. I asked that they be placed in the tree. I looked up some of the SNPs in my Yfull BAM and they are valid SNPs but were not used in my analysis. I don't know why that is. It will be interesting to see where all these new named variants will be placed.

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sat Dec 30, 2017 12:35 pm
This post on the FTDNA forum shows that FTDNA is having problems with the Big Y upgrade and the reason for the delay.

"I called ftdna today and learned that all my outstanding 37->38 redos were actually being rerun from scratch (i.e. back to the lab.) In one case (a guy in Scotland) they are awaiting a new dna sample."

Also
http://haplogroup.org/calling-for-a-big ... nitiative/

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Wed Jan 03, 2018 3:12 pm
A post by Dr Iain on the U106 forum today.

"Hi folks,

"This message is for any BigY testers who had Build 37 BigY results, i.e. those whose results were first delivered before early October 2017, who may have been included in our original BigY analysis spreadsheets and age analysis. Please read carefully!

A new analysis requires comparison on the same Build. Hence, the old Build 37 data you uploaded to the forum needs updated to Build 38.

The Build 38 update at Family Tree DNA now appears largely complete, any outstanding kits appear to be being re-run in their entirety, and we don't expect any changes to the raw data that is being presented. We're pressing forward with talks with Family Tree DNA about how best to do this, either by a bulk download given to us by Family Tree DNA, or by some other means.

The central question here is one of consent. The community, including Family Tree DNA and ourselves, is becoming more rigorous on consent. We hope we have obtained informed consent from each of you to use your raw data as we have. However, in some cases, this consent has been implicit rather than explicit. Depending on how we use your data in future (e.g. if they ever form part of an academic publication), we will be required to show that we have your explicit, informed consent to use your data.

Consequently, I would now encourage you all to upload your new Build 38 data to our data repository:
http://www.haplogroup-r.org/submit_data.php
for further analysis. While from an administrative point of view this may be more difficult, I would rather prioritise the central tenet of informed consent. This will hopefully also let us get ahead with the analysis itself.

Equally, if anyone has previously submitted their data but does not wish to take part in this future analysis, please make your feelings known to the administrative team."

Best wishes,

Iain.

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu Jan 04, 2018 10:26 am
About The Family Tree DNA Database
"Our databases are the most comprehensive in the field of Genetic Genealogy. As of January 4, 2018, the Family Tree DNA database has 928,634 records. Total numbers include transfers from the Genographic Project and resellers in Europe and Middle East. We also have:

9,864 SURNAME PROJECTS 543,249 unique surnames 645,067 Y-DNA records in the database 326,266 25-marker records in the database 304,811 37-marker records in the database 159,777 67-marker records in the database 283,567 mtDNA records in the database 124,794 FGS records in the database."

FTDNA has only 159,777 67 marker records out of 645,067. That was not good enough for finding significant matches. The minimum number of markers that one would have needed without a snp test would be 67 markers.


YSNP tests trump all other YDNA tests especially the Big Y. The Big Y should be the one and only test that should be bought by any newbie. FTDNA intends to extract YSTR markers from the Big Y tests this year so 12,25,37 and 67 marker tests will not be neccesary. They also intend to add the TMRCA for known subclades.

Yfull has the best type of Y tree at present. Testers can see their subclade matches and the country that they are from, the age of the branches and 300 plus ystr marker haplotypes associated with each branch.

Testers who have few or no matches at FTDNA can look at the Yfull tree and look at their upstream branches. Yfull does not have all the known branches of U106 at present due to the fact that a lot of U106 testers with NGS tests do not use YFull.


https://www.familytreedna.com/learn/y-d ... g-y/big-y/

"The Big Y product is a Y-chromosome direct paternal lineage test. We have designed it to explore deep ancestral links on our common paternal tree. Big Y tests thousands of known branch markers as well as millions of places where there may be new branch markers. This product is intended for expert users with an interest in advancing science.

It may also be of great interest to genealogy researchers of a specific lineage. However, it is not a test for matching you to one or more men with the same surname in the way that our Y-DNA37 and other tests do."

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Fri Jan 05, 2018 11:21 am
A post at FTDNA yesterday with a very unhappy customer. http://forums.familytreedna.com/showthread.php?t=42814

I checked the FTDNA tree today for A8039. All of these testers in this group below are SNP matches. Clicking on "more" on the FTDNA tree will bring up more SNPs.

A8039
R-A8039
A8040
R-A8040
A8041More...
R-A8041
BY11762More...
R-BY11762
A8045More...
R-A8045
BY12548
R-BY12548
BY14094
R-BY14094
BY14091

Yfull has only two testers with the A8039 SNP but the TMRCA is 4,400 YBP. https://www.yfull.com/tree/R-A8039/

On my Big Y matches page it shows 5 levels and I can look them up at Yfull. I have only one match at FTDNA due to the 30 SNP threshold but I know that the next level up I have more SNP matches which can be seen in the YDNA projects. And a google search of the SNP will take up all or any info about it.

Michael Sager at FTDNA deals with the FTDNA tree.


Also, a tip for finding subclade matches at semargl.me.

Enter your ID at semargl.me and click on search;
It shows 12,25,37,67 and 111, click on 67;
In the box enter 10 instead of 15 and click on search;
MAX GD (The method of infinite alleles):10

Anyone who matches within the 57 out of 67 markers threshold should be in the same subgroup and the TMRCA for that group could be between 1,000-2,000 ybp. Look for patterns and anyone who is U106 should look for the 66 marker DYS492=13. The threshold can be lowered if one finds that they have closer matches than 57/67.

You can click on the matching ID and see if they are in a project or else take a note of the IDs that match and look for them at google. And if that fails you can still take note of their MDKA and create your own cluster map.

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Fri Jan 05, 2018 8:03 pm
FTDNA's Y tree needs to be modelled on the Yfull Y tree or a similar type Y tree to accommodate Big Y testers.
They may have a problem making a testers FTDNA ID public but they may be able to create a Big Y ID similar to Yfull.
The flag idea is good because it shows where the testers MDKA ancestors originate and the TMRCA's ,while not perfect, are a good start.
The projects may need a new format for Big Y testers.
Some testers are not keen on joining the projects because they have other tests on the same pages like FF and MTDNA FS which can be viewed by project admins.
NGS tests are the future and if testers are not willing to share then they should not dna test in the first instance. They will learn nothing by keeping their data to themselves.

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sat Jan 06, 2018 9:09 am
https://www.familytreedna.com/faq-markers.aspx
How Many to Test? 12, 37, 67 Markers?

"Family Tree DNA wanted to ensure our customers that by testing with us they could obtain the highest resolution Y-DNA test in the world (like FTDNA clients may also obtain the highest resolution test on their mtDNA by taking our Full Genomic Scan, which looks at the entire mitochondria molecule).
Several groups of families have still not been able to completely determine the relatedness of group members with our flagship 37 marker test. Therefore we see two main advantages of testing 67 markers over testing 37:
Y-DNA67 can further refine our estimate of how closely related two individuals are,
By using additional markers groups of related participants have a better chance of finding mutations which identify sub-branches in the family.
However, not all participants or projects need to test 67 markers in order to achieve their objectives.

Some projects will be able to achieve their goals with a 12, 25 or 37 marker test. Only if you are in a project and part of a subgroup of that project where you match, exactly or nearly exactly, to several others will you gain by upgrading to additional marker.

Our motto could be: test only what you need, upgrade only when necessary."

FTDNA got it wrong in their FAQs. A 67 marker match will not show how closely related two testers are. NGS tests like the Big Y will show if two testers are related. YSTR tests are only a guide. YSTR tests were okay when there were no YSNP tests but YDNA testing has moved to a new level. If the Big Y was available as a test 11 years ago when I bought my first 12 marker test, I would have bought the Big Y and myself saved a lot of money through unnecessary SNP testing.

When I eventially found my first 67 marker match he had a different surname to mine and it was only through Big Y testing that we found we are separated by 1,300 years. That is an estimated TMRCA. FTDNA states that a match at 67 markers is within a genealogical timeframe but that is only for two testers with the same surname,perhaps.


I think that the Big Y and other NGS tests will prove to be the best tests to prove that two testers are related within a genealogical timeframe , in the not too distant future. The SNP packs are only stop gaps because one is testing other peoples SNPs. Eventually one will have to go for a NGS test and they will have wasted time and money.

DNA testing is a hobby for a lot of people and some people need to chill out. For me it has been a journey into the past and I am still learning new stuff every day. Any foolish thoughts I had about being related to Irish Kings or whatever eleven years ago, have long since evaporated. Finding out if I was related to Niall of the Nine Hostages brought me into dna testing. I don't know what goal other testers have, but mine is to try and establish the pathway of my Y ancestors into the Isles and the timeframe. I can't achieve this without the help of other ydna testers who are willing to share their results.

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Tue Jan 09, 2018 1:53 pm
A reply from FTDNA in answer to a request for my Hg38 BAM.

"Thanks for contacting us. Unfortunately, BAM files will not be produced until after the update is completed for all testers. Once the update has been completed, we recommend viewing the new information and tools and then requesting the new BAM file if still necessary. We will send a notification once BAM files will be available again. I apologize for the inconvenience.

Posts: 2099
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Wed Jan 10, 2018 7:48 pm
Gioello
I had a new Big Y match today. He has broken up the 23 SNP block of SNPs that I share with my first Big Y match. He is not a YSTR match and we have 26 mismatched SNPs. His most distant known ancestors are from Wales with a ancient Welsh surname. I am pleased that I am not in an SNP bottlenecked branch.

Posts: 2312
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
R- Z2110 (KV7Y2)
MtDNA:
K1a1b1e/HQ176413
PostPosted: Wed Jan 10, 2018 8:57 pm
dartraighe wrote:Gioello
I had a new Big Y match today. He has broken up the 23 SNP block of SNPs that I share with my first Big Y match. He is not a YSTR match and we have 26 mismatched SNPs. His most distant known ancestors are from Wales with a ancient Welsh surname. I am pleased that I am not in an SNP bottlenecked branch.


Glad to know that, but unfortunately without the Big Y and the YFull exam we lack many possibilities. Nothing is sure with the vcf file of FTDNA.
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