Big Y enhancements started Oct 10th

[vinnie]

In one kit I have seen upstream matches that don't show up in the downstream match list. This kit currently has 1 match in the last step and 11 (10 others plus the same 1) in the 4 upstream steps. In other kits the downstream step matches are the ones who have so far shown up.

Thank you for confirming that eventually we'll see these upstream matches as well. Being able to see matches in this format will not only be interesting, but it could be useful for more easily tracking the ethno-geographic development of a subclade.

[vinnie]

Yes, and various permutations involving known variants listed as ancestral but the browser showing all derived, as well as
a location being called but clearly a nocall, or a nocall but clearly either ancestral or derived.

These all look to be in the usual suspect bad areas both on their browser and at the corresponding places on the Build 37 BAM.

According to my revised Big Y analysis, I have 45 high confidence unnamed variants, each of which shows a difference between the reference and the genotype. Should I not accept these results at face value?

[JacqueliFinley]

Z-DNA

I have heard of Z-DNA programs that can alter Y-DNA, how is this done?

[The_Contemplator]

According to my revised Big Y analysis, I have 45 high confidence unnamed variants, each of which shows a difference between the reference and the genotype. Should I not accept these results at face value?

He is just referring to some locations in the Y chromosome that are not reliable. He is not saying that other variants can't be trusted.

[The_Contemplator]

I have heard of Z-DNA programs that can alter Y-DNA, how is this done?

You should make a separate thread if you are not talking about the topic of this thread. Also, I suggest giving more details on what you want to know.

[ljonas]

I have the same unnamed variant but with 13 reads. Mine are all ancestral also.

Thanks! I guess I'll toss that one out. You just saved me a dollar at YSeq since I won't be requesting this from Wish a SNP.

[mwwalsh]

Here is the count of Big Y results by day since the conversions began for those in the R1b project.

10/12 - 116
10/13 - 127
10/14 - 45
10/15 - 51
10/16 - 64
10/17 - 80
10/18 - 99
10/19 - 83
10/20 - 33
10/21 - 63
10/22 - 8
10/23 - 0
10/24 - 21
10/25 - 170
10/26 - 97
10/27 - 133
10/28 - 142
10/29 - 148
10/30 - 104
10/31 - 57
11/01 - 63
11/02 - 89
11/03 - 91
11/04 - 42
11/05 - 40

57 results were completed on 11/06 and so far today we have 43 (almost 8 hours since midnight Houston time).

Overall, the project is now over 66% completed.

[dtvmcdonald]

According to my revised Big Y analysis, I have 45 high confidence unnamed variants, each of which shows a difference between the reference and the genotype. Should I not accept these results at face value?

Unfortunately, no. A simple, unequivocal no.
As a first cut you have to look at the new chromosome browser display. If you see lots of other pink columns
nearly all filled in ... be very leery. If you have any
SNPs listed above position 50,000,000, look at those
for examples of this. No SNP above 50,000,000 is reliable.

Also, there are simple unexplained things... like my own
results list a variant at 9200996, reference G, genotype C.
Yet the browser shows all Gs, and this position is
listed as a nocall in the BED and is not in the VCF at all.
The corresponding location in my build 37 BAM agrees.

At the very least, then you also should check to see that
a SNP you are interested in is in the BED file and looks
OK in the VCF file. The latter takes a bit of guruness.

[dtvmcdonald]

See my previous reply.

I have been examining my now reasonably numerous R1a-CTS4179
files. The BED/VCF files are FAR more reliable than the online fiascos. You can quote me on the word fiasco.

But the VCF is not 100% underestandable ... Has anyone
figured out how the the get the numbers in the "PASS/fail for some reason" column? I can see in general terms why they
list a fail, looking at the other columns to the right.
But not numerically.

Probably when asked they will say "propiertary" but usually
these things can be figured out.

I do see several SNPs that are important to my project
that they are listing as nocalls simply because they now
fall just a tad short of some (not yet figured out by me)
criterion for number of reads.

We need to help each other on this matter. I will also post this on Anthropgenica.

[mwwalsh]

57 results were completed on 11/06 and so far today we have 43 (almost 8 hours since midnight Houston time).

Overall, the project is now over 66% completed.

Let's hope they can keep this morning's pace up all day. They have done 94 from the project so far today. This is rate of about one every nine minutes.

[mwwalsh]

Let's hope they can keep this morning's pace up all day. They have done 94 from the project so far today. This is rate of about one every nine minutes.

It's 6:15pm US CST and we have 145 done today so far. There is hope. We are darn near 70% complete for the R1b project.

[gatty]

This is ridiculous. Still awaiting results from the upgrade. Haplogroup has been moved from E-BY5219 back to E-L17.

[dtvmcdonald]

Big batch of r1b's this morning: now exactly at 3/4 done
Very small batch of R1a'a this morning: now exactly at 2/3 done. They are leaving the most important R1a's for last.

I sent an example of an actual mistake in the new online novel variants display to them.
They list me as being a variant, including on the browser,
when all data, even the browser itself, says I'm reference,
as is everybody else in Q and R. There are other examples.

Caveat emptor.

[mwwalsh]

It's 6:15pm US CST and we have 145 done today so far. There is hope. We are darn near 70% complete for the R1b project.

Here is the latest status for the R1b All Subclades Project.
https://www.familytreedna.com/groups...out/background

Yesterday was the 2nd highest day we've had so far with 164 results converted. This is continuing so far this morning with 128 (edit 10:21am CST) done today. The daily tracking is below. We are at 74% complete as of right now.

10/12 - 116
10/13 - 127
10/14 - 45
10/15 - 51
10/16 - 64
10/17 - 80
10/18 - 99
10/19 - 83
10/20 - 33
10/21 - 63
10/22 - 8
10/23 - 0
10/24 - 21
10/25 - 170
10/26 - 97
10/27 - 133
10/28 - 142
10/29 - 148
10/30 - 104
10/31 - 57
11/01 - 63
11/02 - 89
11/03 - 91
11/04 - 42
11/05 - 40
11/06 - 57
11/07 - 164

Finally, unbelievable, but one of my two Big Y's came in this morning.

Please note.
1) Even though these results may be all converted soon it does little good to look at your Big Y Matches until everyone in your youthful subclades are done.
2) FTDNA says they won't even start making true Hg38 BAM files available until after everyone is converted and typically it takes time to get your BAM file share link once you can request it.
3) There almost has to be kinks, bugs in the system after a migration this massive. I'm expecting a couple of months to straighten those out.

[mwwalsh]

Finally, unbelievable, but one of my two Big Y's came in this morning.

Please note.
1) Even though these results may be all converted soon it does little good to look at your Big Y Matches until everyone in your youthful subclades are done.
2) FTDNA says they won't even start making true Hg38 BAM files available until after everyone is converted and typically it takes time to get your BAM file share link once you can request it.
3) There almost has to be kinks, bugs in the system after a migration this massive. I'm expecting a couple of months to straighten those out.

I do have four new unnamed variants that I didn't have before. I'll have to check this out to see what looks valid and valuable.