What exactly is Yfull?

[richjh]

This was from a member back in 2014.
Rich
If you plan to upload to YFull you will have to use a cloud service like Dropbox, since YFull can't take a direct file upload but requires a url

[The_Contemplator]

Well that is no longer true. You can now just use a share link from FTDNA to transfer your Big Y BAM file to YFull.com. YFull analyzes your Big Y data. Take a look at their site and their tree. Some times they can even place you in a haplogroup branch newer than what FTDNA has you set to.

[ifiru]

They are creating new tree branches too when enough samples are available. And you get much matches different than Big Y matches. There are SNP-matches and STR-matches.

[John McCoy]

In my experience, YFull is way, way ahead of FTDNA. For those who belong somewhere under R-P312, there is also the FREE "Big Tree" web site (ytree dot net), which has made terrific strides in extending that part of the tree, and with many more participants. Are there other projects similar to Big Tree for other haplogroups?

[MMaddi]

In my experience, YFull is way, way ahead of FTDNA. For those who belong somewhere under R-P312, there is also the FREE "Big Tree" web site (ytree dot net), which has made terrific strides in extending that part of the tree, and with many more participants. Are there other projects similar to Big Tree for other haplogroups?

The R1b-U106 Project has been using a specially programmed spreadsheet for Big Y analysis, developed by one of our computer-savvy members. We ask members with Big Y results (currently 756 members) to upload their raw data (VCF/BED files) to the files section of our Yahoogroup for use in the spreadsheet. Almost 90% of the members with Big Y results have done this.

The spreadsheet is far superior to the post-Big Y analysis that FTDNA gives its customers, just as Alex's tree is superior. Over the last 2-3 years, this process has led to discovery of scores of new subclades, as well as letting members with results in the spreadsheet know which of their novel variants don't match anyone and are probably private SNPs that may be useful for their research in a genealogical time frame.

Due to the illness of the member who developed and ran the spreadsheet and the untimely death of the person who took his place in running updates of the spreadsheet, we're in a transitional period now. We're trying to develop better programming for a new spreadsheet and are close to bringing it out of beta. We've also started an analysis program for results from the NGS test that Full Genomes has, which over 100 project members have taken. Finally, we're in touch with Alex about seeing how we might be able to incorporate the U106 project results in his Big Tree.

[wkauffman]

The R1b-U106 Project has been using a specially programmed spreadsheet for Big Y analysis, developed by one of our computer-savvy members. We ask members with Big Y results (currently 756 members) to upload their raw data (VCF/BED files) to the files section of our Yahoogroup for use in the spreadsheet. Almost 90% of the members with Big Y results have done this.

The spreadsheet is far superior to the post-Big Y analysis that FTDNA gives its customers, just as Alex's tree is superior. Over the last 2-3 years, this process has led to discovery of scores of new subclades, as well as letting members with results in the spreadsheet know which of their novel variants don't match anyone and are probably private SNPs that may be useful for their research in a genealogical time frame.

Due to the illness of the member who developed and ran the spreadsheet and the untimely death of the person who took his place in running updates of the spreadsheet, we're in a transitional period now. We're trying to develop better programming for a new spreadsheet and are close to bringing it out of beta. We've also started an analysis program for results from the NGS test that Full Genomes has, which over 100 project members have taken. Finally, we're in touch with Alex about seeing how we might be able to incorporate the U106 project results in his Big Tree.

One other point is that the replacement U106 analysis script will also include haplogroup age estimation capabilities. The BASH/Python solution remains under development but any haplogroup admin is welcome to download it and set it up to support their project. Technically with this script in place there should no longer be a need for individuals to consider going to YFull for age estimates.

[clintonslayton76]

What John McCoy said...

In my experience, YFull is way, way ahead of FTDNA.

Yfull is a Moscow-based operation that grinds exceeding slow but careful. It does not test, and is therefore unconcerned with physical logistics, it is solely interested in generating further "downstream" SNPs to approach historical times.
I consider it as developing more information about newer SNPs than any other service, and I think of downloading my Big Y .bam there as similar to downloading my atDNA to GEDMatch, with this important distinction: it does have a price, and it is not monstrously large (yet).
I have been waiting many months for SNP and STR matches there, but it has brought my terminal SNP down (by their lights) to an estimated 2900-3900 ybp.
I think of this as not replacing FTDNA but leveraging the results for a second opinion from admins who are dedicated to this one task.

[clintonslayton76]

Update

I have been waiting many months for SNP and STR matches there, but it has brought my terminal SNP down (by their lights) to an estimated 2900-3900 ybp.

Two days after entering this, YFull produced 500 STR predictions. I can fill in all 111 FTDNA markers into a spreadsheet, but they will not show on the Project page, because this is not a partner to FTDNA.

[Wing_Genealogis]

YFull STR predictions

Two days after entering this, YFull produced 500 STR predictions. I can fill in all 111 FTDNA markers into a spreadsheet, but they will not show on the Project page, because this is not a partner to FTDNA.

While YFull does give STR predictions for most, if not all of FTDNA's 111 STR markers, the Big Y testing process is no where near as rigorous as the STR testing process used by FTDNA (and others)

Thus, there may well be some errors in YFulls predictions.

While some folks gripe about the fact FTDNA does not use the STR results from Big Y tests, their reasons are precisely due to the fact the Big Y was not developed to capture the STRs, so they are merely predictions, not true results.

[lgmayka]

While YFull does give STR predictions for most, if not all of FTDNA's 111 STR markers, the Big Y testing process is no where near as rigorous as the STR testing process used by FTDNA (and others)

YFull gives Y-STR measurements, not mere predictions.

However, YFull does not perform its measurements the same way FTDNA does--and in fact I'm not sure whether FTDNA has completely and precisely documented its algorithm. So, although YFull generally tries to make its Y-STR counts compatible with FTDNA's, I have observed occasional variances.

The more important points are:
- YFull is unable to measure all of FTDNA's standard 111.
- One cannot directly and easily compare YFull's Y-STR haplotypes against FTDNA's large database.

By the way, YFull has a specific note about Y-GGAAT-1B07:
---
YFull Y-GGAAT-1B07 does not coincide with the FTDNA nomenclature!

Y-GGAAT-1B07 is kind of an oddball. The SMGF laboratory has developed primers for this STR on the AC019099 sequence of the RP11-428D10 clone of the RP11 donor. This sequence doesn’t appear on the human reference genome though. Not even on GRCh37/hg18. We know for sure that the sequence exists in (almost) every male and that it is inherited in a direct male line. Therefore it must be somewhere on the Y chromosome. The 5 bp long GGAAT repeat pattern is very common in the centromeric region of the Y chromosome, but also it is the general structure motif in the Yq12 region. Both of these regions represent huge gaps were we haven't got enough sequencing data in order to create a propper assembly and a consensus sequence from it. Therefore the exact position of the Y-GGAAT-1B07 marker will remain a mystery until we'll have better sequencing technologies that are able to sequence several 10 thousand bases in a row.
Thomas Krahn // link removed
---

[Wing_Genealogis]

Y-GGAAT-1B07 has been mapped in GRCh38

Larry,

As you reported elsewhere last year, Y-GGAAT-1B07, has been mapped to GRCh38 at Y:10687543-10687730.

Your comment about YFull's measurement of this STR being different from FTDNA's measurement is certainly still valid.

[Wing_Genealogis]

In general, it is the longer-read STRs (such as CDY) which are harder for the Big Y (and other NGS tests) to accurately measure.

[malsaqer]

One other point is that the replacement U106 analysis script will also include haplogroup age estimation capabilities. The BASH/Python solution remains under development but any haplogroup admin is welcome to download it and set it up to support their project. Technically with this script in place there should no longer be a need for individuals to consider going to YFull for age estimates.

This is interesting. Is this script still available to download?

[ljonas]

Posted by lgmayka:
"- YFull is unable to measure all of FTDNA's standard 111."

This is easily solved. You need to upload two files to YFull. First, the BAM file. Second the CSV file of STRs. You will then be able to compare in a YFull group all of the first 111 STRs as well as the STRs that were obtained in the Big Y test.