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ICAM2017
03-10-2019, 02:29 AM
In a recent post on one of the FTDNA Group Projects it was stated:

"In the Big Y500 tests, we were generally seeing a new SNP mutation appear about every ~120 years or so. While the data is still being crunched and we need many more files to be released, initial Big Y700 files seem to be averaging a new valid SNP mutation every ~80 years (or 2-3 generations)!!!! That is close to a 30% increase from the old version. An increase like this means that there are now many more possible SNP mutations to help with branching patterns in families in the last few hundred years even. While some of you may still be considering testing strategies, anyone who has done the previous version will certainly be looking at the possibility of upgrading."

My understanding was that the BigY500 DNA Test was able to identify all SNP's both known and Private. Therefore is not the Big Y700 just a better interpretation/reading of the YDNA results.

If that is the case then how does the FGC BAM Analysis (part of the FGC Y-Chromosome Sequencing And Analysis), previously stated as providing the best in market analysis , compare.

JamesKane
03-10-2019, 02:46 AM
The difference in BY700 is not in the analysis of the raw data, but an additional 5.5 million locations being targeted on the Y chromosome. Effectively, they have finally reached parity with the tests FGC was selling about 6 years ago.

I’m sure they would be happy to run their superior analysis of the raw data on one of these newer tests as well.

FGC Corp
03-10-2019, 03:51 AM
The difference in BY700 is not in the analysis of the raw data, but an additional 5.5 million locations being targeted on the Y chromosome. Effectively, they have finally reached parity with the tests FGC was selling about 6 years ago.

I’m sure they would be happy to run their superior analysis of the raw data on one of these newer tests as well.

I'd add that, in my opinion, the only way to substantially improve on "short-read" sequencing, such as BigY700, Y Elite, and 30x whole genome, is through one of the long read approaches.


The difference in BY700 is not in the analysis of the raw data, but an additional 5.5 million locations being targeted on the Y chromosome. Effectively, they have finally reached parity with the tests FGC was selling about 6 years ago.

Welcome to 2013, FTDNA. The highest short-read performance is probably with the 250bp read length approach. We tried that, but the payoff was modest (perhaps 5%). That's why we've been focused on the long read approaches.

For the moment, the 10x Chromium is the most affordable of the long read approaches. PacBio is currently close to $10,000 per test.

claudefrancis
03-11-2019, 08:28 PM
Hi
Just to be clear if you have a file BAM of ftdna and you send it to Full Genomes to analize, FGC can discovered new possible SNP downstream of your branch?

ICAM2017
03-11-2019, 09:33 PM
Hi
Just to be clear if you have a file BAM of ftdna and you send it to Full Genomes to analize, FGC can discovered new possible SNP downstream of your branch?

Thanks for all replies so far. I have had my BIGY500 BAM file analysed by FGC. The question I was really trying to ask was "would BigY700 give me much more information than the FGC BAM Analysis, especially in regard to my known and private SNP's. I have already uploaded my FGC results to Alex Williamson's Ytree, which has not yet been finalised but I can already see there appears to be a lot more information compared to my earlier BIGY500 upload to Ytree.

claudefrancis
03-12-2019, 05:37 AM
I receive my big y700 2 weeks ago and I sended my file BAM to yfull. Honestly about SNP nothing new, just STR
connection with other people. Now I send my file BAM to FGC just to make a confrontation. I am waiting the results.

ICAM2017
03-12-2019, 08:04 AM
I receive my big y700 2 weeks ago and I sended my file BAM to yfull. Honestly about SNP nothing new, just STR
connection with other people. Now I send my file BAM to FGC just to make a confrontation. I am waiting the results.

Will be interesting to see what the outcome is. Could give BigY500 testers an insight as to whether there is a benefit to upgrade to 700 ( Cost not yet established) or if a better bet to upload to FGC BAM analysis for $50.

ICAM2017
03-12-2019, 08:05 AM
I receive my big y700 2 weeks ago and I sended my file BAM to yfull. Honestly about SNP nothing new, just STR
connection with other people. Now I send my file BAM to FGC just to make a confrontation. I am waiting the results.

Will be interesting to see what the outcome is. Could give BigY500 testers an insight as to whether there is a benefit to upgrade to 700 ( Cost not yet established) or if a better bet to upload to FGC BAM analysis for $50.

JamesKane
03-12-2019, 08:40 AM
FGC's analysis of the Big Y 500 data mostly gives you access to a standardized variant discovery pipeline, without dropping 300,000 lines of raw data on you in VCF format. On older samples you would find additional SNPs since FTDNA's calling threshold for number of reads is at least 2x deeper than accepted in academic circles. Part of this is because FTDNA uses their own proprietary alignment and variant discovery software. In the end all FGC is doing is using a more proven pipeline and incorporating a better set of quality metrics to get more out of your existing data.

There's no magic that can be done to match the new coverage in the updated test. If you want to know what's in the remaining 5.5 million bases, you'll need more sequencing done. That's the whole reason I have been recommending people look at purchasing the solutions with the lowest $/allele ratio not the least total cost for years.

claudefrancis
03-12-2019, 10:31 AM
I don't understand FGC with file BAM of ftdna can explain better the file BAM as Yfull ?
If yes because FGC have more database SNP and STR as yfull ?

Wing Genealogist
03-12-2019, 11:00 AM
I don't understand FGC with file BAM of ftdna can explain better the file BAM as Yfull ?
If yes because FGC have more database SNP and STR as yfull ?

With regards to analyzing the Big Y results, YFull and FGC are (by and large) similar. The big difference is the fact FGC also has their own suite of tests (Y-Elite, Whole Sequence, Long Read, etc.) while YFull only has their analysis service.

Most people really want to see how their results compares with others. As such, the size of the database (particularly for your subclade) is important. In this regard, FTDNA has a MUCH larger database than either YFull or FGC.

claudefrancis
03-12-2019, 11:37 AM
Dear Wing Genealogist,

you explain me that with the file BAM of FTDNA, FGC can maybe explain better some SNP or new SNP idem for STR.
But for the confrontation with this SNP, new SNP or STR is better FTDNA ?
The problem with FTDNA is that this company promote only Big Y test or Y STR test. Nothing of SNP or pack SNP
FTDNA have old pack SNP and make nothing for clients, the clients must go to yseq to make single test SNP !

FGC Corp
03-12-2019, 04:17 PM
Dear Wing Genealogist,

you explain me that with the file BAM of FTDNA, FGC can maybe explain better some SNP or new SNP idem for STR.
But for the confrontation with this SNP, new SNP or STR is better FTDNA ?
The problem with FTDNA is that this company promote only Big Y test or Y STR test. Nothing of SNP or pack SNP
FTDNA have old pack SNP and make nothing for clients, the clients must go to yseq to make single test SNP !

FGC can now do single SNP tests. You can email us at support [at] fullgenomes [dot] com

claudefrancis
03-12-2019, 05:23 PM
Dear FGC Corp,

After the results of FGC of my file BAM of Big Y 700 I will test some SNP by FGC maybe more. I can just say FGC is very smart to answer and clear in particular Justin.

FGC Corp
03-12-2019, 07:10 PM
With regards to analyzing the Big Y results, YFull and FGC are (by and large) similar. The big difference is the fact FGC also has their own suite of tests (Y-Elite, Whole Sequence, Long Read, etc.) while YFull only has their analysis service.

Most people really want to see how their results compares with others. As such, the size of the database (particularly for your subclade) is important. In this regard, FTDNA has a MUCH larger database than either YFull or FGC.

As you already know, the FTDNA database does not include data from FGC and other labs. It is also incomplete in that regard. Plus, as well, the U106 tree (maintained by the R1b-U106 team) is better than the FTDNA U106 tree.

The only option for customers to compare FTDNA and non-FTDNA data is with other companies, such as FGC or Yfull (or with independent projects such as https://www.ytree.net maintained by Alex Williamson for R1b).

claudefrancis
03-12-2019, 10:59 PM
I am at the moment I-A6397, but I have into my file BAM of ftdna about 42 unnamed SNP. Some incomprehension about STR. Yfull not explain me this situation. This is the reason why I want the point of view of my file BAM by FGC. After if there is some new SNP I will test it by FGC!