Another Reason Not To Use Dante Labs

[Webmaster]

Dante Labs has been plagued with quality control and bad customer service issues since they first hit the genetic genealogy community a couple of years ago. Now, they are flatly saying their service is not primarily intended for genetic genealogy and are not making it particularly easy to use their WGS test results for genetic genealogy. When someone recently contacted Dante Labs about obtaining their BAM files, this is an abstracted reply they received.

Thank you for contacting Dante Labs.

As you know, our test is not focused on ancestry information, in general, although the raw data are compatible with some ancestry services like MyTrueAncestry and YFull, as mentioned. In that case, you could use the snp.vcf file.

Thanks.
​Kind regards
Dante Labs Customer Support Team

So Dante Labs kind of ducked the original question of how to obtain the BAM files. But to quote YFull:

NOTE: The data extracted from the .VCF file is incomplete. ~ 50-70% of data that can be taken from the .BAM file
[ https://yfull.com/ ]

Further, Dante Labs is still using the very outdated hg19 human genome reference for their results, whereas most other companies are using the newer hg38 reference. So, IMO that should completely eliminate Dante Labs from consideration for sequencing labs for genetic genealogy.

The only 2 companies I am aware of that have reasonably priced WGS tests are YSEQ (WGS400 - 15X, but almost double standard read lengths, which can greatly improve accuracy) and Nebula Genomics (Deep Test - 30X, but standard read lengths). I have no experience with Nebula Genomics, but have done the WGS400 test at YSEQ and was pleased with the process and results. Also, AFAIK, Nebula Genomics is still using Chinese sequencing labs to do the actual sequencing, while YSEQ does the sequencing in Germany.

[zackdaugherty]

I tested my father's DNA at Dante early on but I think he was somewhat lucky after all that I read. I was able to get the BAM and everything but even though well ahead of the test completion I asked for HG38 they gave me HG19. I then had to hand it over to Thomas at YSEQ to remap it (which was $20 well spent as he also does a QC check on novel variants and adds them to YSEQ catalog and YBrowse).

But overall from all that I've read and various inconsistent poor quality reads below the promised 30x I simply couldn't recommend them. Any future WGS I do will probably be with Thomas at YSEQ.

[Webmaster]

As a follow-up, Dante Labs directly transferred the individual's hg19 BAM file, which apparently includes both Y-DNA and MT-DNA, to YFull, but did not provide a copy to the individual. The individual is still trying to get the hg19 BAM file transferred to the Y-DNA Data Warehouse for processing and posting on The Big Tree by Alex Williamson, but so far that is not happening.

Dante Labs completely side-stepped getting the hg19 BAM file to YSEQ to "lift" it to hg38, which you had done for your father's data, Zack. They are being deliberately unhelpful about anything except getting the hg19 BAM file to YFull. Definitely not recommended at all!

[zackdaugherty]

No doubt, sounds terrible.

As a side note I had taken my father's lifted HG38 WGS after Thomas remapped it, had James Kane at Y-DNA Warehouse format it best for Alex Williamson when adding it to the warehouse 3 years ago. Unfortunately Alex (3 years ago) told me he wasn't adding WGS like this to the Big Tree - but that he would eventually. I inquired about it about a year ago and he says it is still planned, but it still hasn't happened yet. So I wouldn't hold ones breath on a WGS getting on the Big Tree anytime soon.

[Webmaster]

Zack,

Alex is adding WGS data to The Big Tree. IDK if he is doing all WGS data or only those who ask him to. James Kane is making gVCF files for Alex to use. As an example: http://www.ytree.net/SNPinfoForPerson.php?personID=12276

[zackdaugherty]

Glad to hear. After hounding him about my father's after James did the same thing 3 years ago creating a gVCF for Alex he still hasn't added him. I finally broke down and Big Y 700 tested my father (mostly to see the Y111 markers for a blog I'm writing on doing a Y-DNA based Mutation History Tree within a genealogical period). My father, Kit 522538, had his Big Y complete last night and I just added his VCF to Warehouse this morning.

So hopefully he'll finally now be included on Alex's tree and I'll finally be able to see the extra combBED Y-SNP I have (B121647) that my father is Negative for.

[Mark Monroe]

@Zach: Could you post a link to your blog? It sounds interesting!

[zackdaugherty]

I haven't wrote it yet, lol. It is simply planned. But I'm wanting to Y-STR and NGS test 1 more descendant that branched away from me at my 4th great grandfather.

I blogged a bit about doing this with only Y-STR (Y111) markers a few years ago here: https://www.odohertyheritage.org/post/p ... -2-12-2019

Now I'm simply wanting to follow-up on it where I examine the STRs AND the SNPs - where each developed down to me, etc. It is an exercise I wouldn't recommend everyone spending money on (but I do think it is good if a person with a semi-distant brickwall try to test patriline descendants that branched away from one another through different children of the brickwall).

[Webmaster]

Zack,

I played around with Dave Vance's SAPP Tool for my major sept that the genealogies say was formed as early as ~700 AD or so. What I found is that SAPP uses the potentially biased modal haplotype derived from all kit entries. This means that if one branch has more kits, it will skew the modal haplotype significantly and cause strange results.

But if one sets the modal haplotype manually, that can be corrected. After tweaking all the inputs, including clade/haplogroup data, it produced a very reasonable result. Of course, there is always the danger of expectation bias. But it is still an interesting tool to see how the STR and SNP data work together.

[zackdaugherty]

I found similar. I update and operate one for entire Doherty Group 1.1.0.0 and all its subgroups (~200 testers with 60+ Big Y tests). It takes a lot of work to maintain and is getting unwieldy. However, the STR estimates to the root actually aren't too far off from the SNP age estimate for BY471 (~950 AD). So I was quite impressed.