BigY700 & FGC Bam Analysis

[ICAM2017]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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 ?