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View Full Version : YFull Has Begun Analyzing Big Y VCF Files With A Free Upgrade to Bam Files Later On.



JMcB
01-13-2018, 06:36 PM
As announced on their Facebook Page:

YFull is very pleased to announce that it will now analyze BigY VCF files. This analysis is only available to persons who for some unknown reason are not able to obtain their BigY BAM files.

The cost of the analysis is $49 and this includes a free upgrade when the BAM files are later submitted to YFull.
VCF analysis can be ordered by using the YFull order form: https://www.yfull.com/order/ .
The complete VCF analysis will be ready after one day. Payment is not required at the time of the order but only when the VCF analysis is ready.
The analysis will consist of information in these categories: Hg and SNPs, Novel SNPs, SNP matches, STR results and STR variants. Please note that a VCF file only contains about 50% of the data that can be obtained from a BAM file.
The $49 cost also includes positioning on the YTree and the ability to join YFull groups. If the analysis discovers any new shared SNPs, these will be added after the next regular update of the YTree.
A VCF analysis does not include age estimation or STR match information.

Only new BigY samples are eligible for VCF analysis. VCF analysis will not be provided with respect to samples already in the YFull database.

Cofgene
01-14-2018, 01:21 PM
Danger - Yfull will name all of the SNPs they "find". They already seem to be plastering unneeded names on recent SNPs named by FTDNA. They will not name other variants which are in the result. If your haplogroup admin would work with FTDNA you would have any new shared SNPs identified and on the tree. Save your $$ and use it to get a SNP test or two in place for some of your STR matches.

GarethH
01-14-2018, 02:11 PM
Danger - Yfull will name all of the SNPs they "find". They already seem to be plastering unneeded names on recent SNPs named by FTDNA. They will not name other variants which are in the result. If your haplogroup admin would work with FTDNA you would have any new shared SNPs identified and on the tree. Save your $$ and use it to get a SNP test or two in place for some of your STR matches.

They are applying a quality filter. They have declined to name one of the three SNPs on my unnamed variants page at FTDNA and have not given names to any of my 22 "ambiguous" SNPs (which FTDNA doesn't recognise at all). They have however given a name to a variant which is "rejected" on my vcf files (both old and new), which has nevertheless passed their criteria. I think it's useful to be able to compare the outcomes of two different approaches to quality filtering. If YFull are naming SNPs already named by FTDNA then it's because FTDNA have been slow to share the details with YBrowse.

Joe B
01-14-2018, 05:28 PM
One reason to consider using YFull is they provide both Hg19 and Hg38 positions. That's useful for matching to samples outside the FTDNA database.
This youtube video of is from YFull. It's from last March so it doesn't include some recent new features.
YFull.com (Take a tour)
https://www.youtube.com/watch?v=NPmFil4WLww&feature=youtu.be

lgmayka
01-14-2018, 11:54 PM
Once one has spent many hundreds of dollars on the Big Y, it seems foolish not to spend $49 for a second opinion on its meaning, especially since FTDNA's haplotree
- Usually times out before displaying
- Is not publicly hyperlinkable.

TigerMW
01-16-2018, 07:58 PM
I already have an Hg19 BAM file on file with YFull. I will pay for the $18 or $19 re-interpretation and re-submit my Hg38 BAM file when it comes in.

I thought about submitting my Hg38 VCF file right now but decided it against it. I can already see the Hg38 VCF data without much problem but it is the very low coverage reads that are only in the BAM files that I think are most important. That's the YFull value-add from my perspective. I don't know if the re-interpretation price applies to VCF files anyway.

It's seems strange that they went from the purist BAM file analysis approach to accepting VCFs but they have to do what the have to do.

I agree, for a $500 test, a $49 second opinion is worth it. One can work with the free BAM utilities or struggle through the Big Y Chromosome Browser kinks and chinks (in the armor) but to me the $49 is not much to pay for a professional perspective.

01-16-2018, 08:10 PM
Any update on when ftdna will be releasing their BAM files? for us recent Big Y folk?

lgmayka
01-16-2018, 11:53 PM
It's seems strange that they went from the purist BAM file analysis approach to accepting VCFs but they have to do what the have to do.
This is an innovative way to maintain some income while waiting, month after month, for FTDNA to finish its hg38 conversion and begin generating BAM files again.

JMcB
01-17-2018, 01:01 AM
Any update on when ftdna will be releasing their BAM files? for us recent Big Y folk?

Hello sgdavies,

I heard on the I-M253 Facebook page, that they’ve been telling people they won’t be out until the spring. While it is hearsay, it’s all I’ve heard at this point.

01-17-2018, 09:35 AM
Hello sgdavies,

I heard on the I-M253 Facebook page, that they’ve been telling people they won’t be out until the spring. While it is hearsay, it’s all I’ve heard at this point.

Thanks JMcB,
hmm so maybe I should toil with the idea of uploading the .vcf, then uploading the BAM at a later point.
any thoughts on this?
cheers.

lgmayka
01-17-2018, 10:07 AM
hmm so maybe I should toil with the idea of uploading the .vcf, then uploading the BAM at a later point.
any thoughts on this.
Makes sense.

Cofgene
01-17-2018, 10:21 AM
Thanks JMcB,
hmm so maybe I should toil with the idea of uploading the .vcf, then uploading the BAM at a later point.
any thoughts on this?
cheers.

Simple sucker marketing. You have so many OCD people who want to see another result now they pay to have the VCF parsed to say they are on YFull's limited tree. Consider the backlog and griping that will occur once the BAM files become available... YFull won't have the compute resources to handle the influx of BAMs and once again the world will hear the griping about delivery of BAM analysis results - except this time YFull is the target.

Pylsteen
01-17-2018, 10:35 AM
This may be their solution for what otherwise would be a long period without income from (FTDNA) BAM files. I think I'll wait, though I am eager to know too.

gotten
01-17-2018, 01:02 PM
Simple sucker marketing. You have so many OCD people who want to see another result now they pay to have the VCF parsed to say they are on YFull's limited tree. Consider the backlog and griping that will occur once the BAM files become available... YFull won't have the compute resources to handle the influx of BAMs and once again the world will hear the griping about delivery of BAM analysis results - except this time YFull is the target.

FTDNA has them (and us) in a neck lock since October. Most of us can patiently wait for the .bam's to become available, but Yfull still need to pay the bills. Even though it will create more work (and potentially delay) I uploaded a .vcf today to support them (and of course to take a peek at the limited results when available).

Pylsteen
01-17-2018, 01:32 PM
FTDNA has them (and us) in a neck lock since October. Most of us can patiently wait for the .bam's to become available, but Yfull still need to pay the bills. Even though it will create more work (and potentially delay) I uploaded a .vcf today to support them (and of course to take a peak at the limited results when available).


I think I'll support them too by sending vcf; they are good; (and more Dutch needed).

01-17-2018, 02:57 PM
I think I'll support them too by sending vcf; they are good; (and more Dutch needed).

yep, ordered.

lgmayka
01-17-2018, 04:25 PM
FTDNA has them (and us) in a neck lock since October. Most of us can patiently wait for the .bam's to become available, but Yfull still need to pay the bills.
If I were not absolutely convinced of FTDNA's moral rectitude, I might suspect that the multi-month delay in BAM files was a deliberate attempt to drive YFull out of business.

No, I don't believe it's deliberate.

JMcB
01-17-2018, 06:00 PM
If I were not absolutely convinced of FTDNA's moral rectitude, I might suspect that the multi-month delay in BAM files was a deliberate attempt to drive YFull out of business.

No, I don't believe it's deliberate. But FTDNA's long and utterly unexplained delay may have that result anyway.

Let’s hope not because they’re a good company that’s constantly trying to improve their customer’s experience. And if the old saying stands, “imitation is the sincerest form of flattery” than FT, perhaps unwittingly, is paying them a compliment because they’re imitating everything that YFull has been doing.

Besides, if YFull goes, I won’t be able to see any matches at all.

So I say, support them all you can!

gotten
01-17-2018, 06:10 PM
The .vcf that I uploaded a few hours ago has already been parsed through their system.

SNPs (all): 114805
Positive: 1932 (1.68%)
Negative: 89192 (77.69%)
Ambiguous: 25 (0.02%)
No call: 23656 (20.61%)

STRs (all): 587
Reliable alleles: 204 (34.75%)
Uncertain alleles: 24 (4.09%)
N/A: 359 (61.16%)

41 out of the standard Y111 were detected as reliable. 12 out of Y37. All 12 STR markers match the result of the Y37 test that was previously done by this kit.

Novel SNPs (all): 18
Best qual: 14 (77.78%) [6 (33.33%) - best; 8 (44.44%) - acceptable]
Low qual: 4 (22.22%)

No STR matches until the .bam is available. Not too bad for a .vcf.

Celt_??
01-17-2018, 06:53 PM
And if the old saying stands, “imitation is the sincerest form of flattery” than FT, perhaps unwittingly, is paying them a compliment because they’re imitating everything that YFull has been doing.....So I say, support them all you can!

I agree with supporting Y Full; I sent them my BAM file a year ago. They do place one's data on their tree fairly quickly and place a [NEW] after it until a human has reviewed it in detail. The data they provide is presented better than FTDNA's is - at least I can understand it better. And I think that Alex's The Big Tree presentation is also better than FTDNA.

The Big Tree: 20888

Y Full: 20889


lgmayka: If I were not absolutely convinced of FTDNA's moral rectitude

I am beginning to have my doubts because it appears to me that marketing is at the forefront of FTDNA's strategy. Witness: 1) their limited interpretation of STR results resulting in so many men as "predicted R-M269", etc.; 2) FTDNA's technical description of the Big Y emphasizing it's "intended for expert users with an interest in advancing science" and "it is not a test for matching you to one or more men with the same surname". Yet Big Y results are displayed with "Matching" as a prominent feature. And, in my case, the Match results are limited to members of my surname project. Under their new criteria, I suspect this is the case for most Big Y testers. JMHO

01-18-2018, 09:11 AM
yep, ordered.

I am on the tree, hanging from a lonely branch :P
20903


Y-Haplogroup: R-Z283*
Terminal SNPs: Z283/S339/PF6217 • Z662/CTS11197/PF6225

I think this pretty much ends my Y journey, I will of course upload my BAM, once its available. Roger out/

lgmayka
01-18-2018, 10:55 AM
I think this pretty much ends my Y journey
Only until a match, even a distant one, occurs. In 2016 a Ukrainian tested Z280*. Hope of any match seemed slim, partly due to conditions in that country. But just recently, a western European tested Z280* and appears to be a distant match. He ordered the Big Y, and I expect that the two of them will form a new subclade, though probably an ancient one (over 2000 years old).

Celt_??
01-18-2018, 03:09 PM
I think this pretty much ends my Y journey, I will of course upload my BAM, once its available. Roger out/

As mentioned, I have been on Y Full and The Big Tree for a year during which time the number of men under R-CTS9733 has double. Thus my position had moved around a lot as my Terminal SNP changed. Here's a series of screen shots from The Big Tree:

DEC 2016: 20908

JUL 2017: 20909

NOV 2017: 20910

Afshar
02-22-2018, 08:50 AM
Anybody knows the origin of the ELT samples that are recently added?

dtvmcdonald
02-28-2018, 07:59 PM
Has anyone besides me tried to get them o release publicly, either to requestees or just to
Ybrowse, the particulars of their DYR STRs, i.e. at minimum locations and the allele number
of HUGO? (build 38)

This is frustrating.