Dante Labs

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Vlad82

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Dante Labs is a pretty new company on the market.
They offer 3 or 4 test https://www.dantelabs.com/collections/our-tests
The most important test for Genetic Genealogy purposes is Whole Genome Sequencing.
Dante Labs offers WGS at a discounted price of 399€, while in some periods it is even lower 349€.
Currently, they have Halloween Special Offer(WGS at only €349): https://www.dantelabs.com/collections/our-tests/products/whole-genome-sequencing

Probably this is the lowest price for WGS at the market.

WGS consists of data for all chromosomes, BAM file can be analyzed by Yfull, both Ydna and mtdna.
Dante Labs WGS has good coverage of Y chromosome, and provide enough information about SNPs.
For comparison, Big Y has two times shorter coverage of Y chromosome and no mtdna. So you have less information even about SNPs.
Yseq WGS is somewhat better because of the length of reads (100 nucleotides and 150 nucleotides), especially for scoring STRs, but also more expensive.

Except for information that can be used in Genetic Genealogy, it is also used for health purposes. Dante Labs provides a free report for wellness, longevity, and rare deceases.
 
Is it possible to "extract" the autosomal, mtdna,ydna and upload it to other sites for matching?
 
I continue following this thread. Any comparison between Dante and Living DNA? I understand Dante offers full genome sequencing. But in practice, is it useful now? As asked in the post above, is it possible to extract the information for useful purposes, right now?
 
jlw and Farstar,
Yfull is a company that can do an analysis of NGS test including Dante Lab WGS, it cost $49
Unfortunately, they do not do autosomal analysis only Ydna and Mtdna.
For Y dna they can find your position on the haplotree, calculate approximate time to your the most recent ancestor with other tested people in your haplogroup. You will also get 10-20 SNPs that are unique to you, some of the SNPs will become new branches when they find someone else who share one or more SNPs with you.
Anyway, when you get haplogroup and SNPs it desirable to contact the administrators of your haplogroup project at FTdna and ask them to check if there is in the project someone who share SNP with you but not on Yfull tree.
Yfull will also provide you about 500 Y-str markers, you can use 111 or less of them for comparison with people tested at FTDna.
For Yfull analysis you will need BAM file, they do not accept VCF files.

If you know how to convert VCF file from HG38 to HG19 or ask Dante Labs to provide you it in both formats you might be able to upload it on https://genesis.gedmatch.com/login1.php
I think then you can use some autosomal calculators from the Gedmech and look for relatives.
I did not try it.

Living DNA does not give you so much information about Ydna and Mtdna, only basic haplogroups.
Anyway, it is not bad to take test at different companies including Living DNA because you will have access to their ethnicity calculators and above all their DNA base to look for relatives.
Gedmatch is trying to become a place where people tested at different companies can compare results, and make it easier and cheaper.
 
Vlad82 said:
jlw and Farstar,
Yfull is a company that can do an analysis of NGS test including Dante Lab WGS, it cost $49
Unfortunately, they do not do autosomal analysis only Ydna and Mtdna.
For Y dna they can find your position on the haplotree, calculate approximate time to your the most recent ancestor with other tested people in your haplogroup. You will also get 10-20 SNPs that are unique to you, some of the SNPs will become new branches when they find someone else who share one or more SNPs with you.
Anyway, when you get haplogroup and SNPs it desirable to contact the administrators of your haplogroup project at FTdna and ask them to check if there is in the project someone who share SNP with you but not on Yfull tree.
Yfull will also provide you about 500 Y-str markers, you can use 111 or less of them for comparison with people tested at FTDna.
For Yfull analysis you will need BAM file, they do not accept VCF files.

If you know how to convert VCF file from HG38 to HG19 or ask Dante Labs to provide you it in both formats you might be able to upload it on https://genesis.gedmatch.com/login1.php
I think then you can use some autosomal calculators from the Gedmech and look for relatives.
I did not try it.

Living DNA does not give you so much information about Ydna and Mtdna, only basic haplogroups.
Anyway, it is not bad to take test at different companies including Living DNA because you will have access to their ethnicity calculators and above all their DNA base to look for relatives.
Gedmatch is trying to become a place where people tested at different companies can compare results, and make it easier and cheaper.
Click to expand...

Vlad82, thanks to the thread you've start and the very useful information you offered, I began to read some more about Dante's WGS 30x test. I've found some interesting discussions about it, sharing pros and cons, I even ended up reading about the sequencing machines and the tech behind the tests.
I think the actual price tag 226£ (259€) is very tempting, yet it will require some further investment to have the results analyzed, still a very good value if compared with other similar tests performed by well established companies.
I ordered my kit 2 weeks ago and had it shipped back to them.
I wonder how big the *bam, *vcf and *fastq files might end up, plenty of space on my hard drives, yet a bit worried about the time required to download them from their cloud.

I am quite aware the Dante lab is sequencing in China the samples, perhaps the operating costs there being lower than elsewhere in Europe or US, and I speculate now that the kit's price is competitive not because of some third parties might co-financing the process due to some some hidden agenda, but I see it as an worthy effort in offering an alternative to the other well established sequencing technologies.
Yet I am fully aware that in the end, you get what you pay for, so I fully understand the test perhaps won't have the accuracy of a 30x by FGC or YSEQ as it might be still a very young and under development tech.
But I hope it will come as accurate as the BGI-500 Seq tech is able to provide at this very moment.
 
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Four and a half months later that day when my kit arrived to the lab, about two weeks ago, I got an e-mail from Dante Labs telling me the reports are ready.

I don't know what should I start with, as I have mixed feelings and the main one is they always listen to their customers but having a "patch up" policy and not a great product from all points of view ready out of the box.
The promised .bam and .fastq files are still to be delivered, if they will eventually-I hope so :D, or I might have to order a hard drive and have them on a physical support. With Dante Labs everything is so relative from one kit to another, from one person to another the experiences vary quite a lot, I think each and everyone who ordered a test from them has their own specific experience with goods and bads.
Some experienced very long delays more than 8 months in some cases, some ordered a hard drive to have their .bam and .fastq files delivered on a physical format. Among these, some still waiting for the hard drive after more than 6 months, while others got their hdd quite quickly.Some others got their .bam and .fastq files in their account ready to be dowloaded quite quickly.

I got one initial report and 4 files(snp.vcf, indel.vcf, cnv.vcf and sv.vcf) ready to download, they call these files "raw results" which obviously they're not. Following instructions from a facebook group dedicated to Dante Labs customers, I was able to download other 5 files( raw.snp.vcf, g.vcf, raw.indel.vcf, sv.xls and cnv.xls) by modifying the URL name of the downloading file accordingly. Later these files became unavailable. But then after people starting to complain about it on that group, the lab created a form and those looking to have these last 5 files available will apparently have them unlocked. But.... only by using the same trick changing the URL and not by having direct links for download like for the 4 official files....wtf ???
Links to other two reports were not functional and the status of my kit was still "we received your kit " like 4 months ago, which was obviously 4 months old news.
Two months ago there was another form to be filled for those who wanted to have their results aligned to HG38. I filled that form but the vcf's I downloaded are all based on the obsolete HG19 ... I am really curious if/when I will get my .bam/.fastq will it be aligned to HG19 or HG38.
Some of the kits being sequenced by BGI in China, seems the raw files are there and it takes time Dante Labs to have em sent to the lab in Italy, I guess they get only these 4+5 files from BGI and maybe the .bam and .fastq ONLY if/when anyone asks specifically for these files.

One day ago I got another mail from them telling me about some new AI report which is to be purchased separately, but checking my account again today I just noticed the links to the 2 missing reports were fixed and I managed to download them.
My kit's status from "we received your kit" jumped over " QC completed" and "Sequencing completed" [it was obvious these stages were reached long time ago...] to " Report ready"... the very last stage.

I left more than a week ago to their customer support a message regarding my .bam and fastq files, got a very quick reply from the first line support telling me they escalated the ticket to the second level support..but no update since back then.

I have the feeling you always have to knock their door and ask for something which should be delivered from the very beginning.
Those from the facebook group who managed to get their bam and fastq files claim that some kits were sequenced at 150 bp while others at 100bp. Comparing the y-dna sequenced by Dante Labs/BGI with the ftDNA's BigY500 it appears the Dante Labs sequencing (BGI)is going 25-30% more in depth, being on par (if not a slight better) than newly introduced ftDNA BigY700.

Checking the header of my raw.snp.vcf file I determined that the actual date when the lab (BGI China) start sequencing my sample was back in mid April !!!! Took them more than 2 months to have my partial results in the lab !!!
As I said I have mixed feelings, it seems to be a great quality sequencing but it is spoiled by all kind of drawbacks and that feeling that you have to use pliers to pluck/to obtain what is advertised while product sold.

I think once they will be able to get rid of that "patching up" model of business they will have one of the best products on the market in terms of value for money spent.

I'll be back with an update once bam and fastq files available (could be days, weeks or many months from now)

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@domogled I have also mixed feeling about Dante Labs. Now I would not recommend anyone to order their tests.
Everything seems to going well in begining, they provide vcf files and reports about 4 months after day of receiving samples but it is almost impossible to get their hard disk with raw data (BAM and FASTQ), I ordered/requested hdd in November last years and still waiting, it seems that more then 90% od people who ordered hard discs still waiting. Without BAM and FASTQ files this test is useless.
 
I am so sorry you are among the ones waiting for the HDD with the raw files all the way back since November. I understand that it is a cue line for the hdd orders, but the only reasonable explanation I see is the lab who sequenced your sample (BGi most probably) not delivering the hdd or simply deleted your raw files. it doesn't make any sense to keep on the cue someone for 7 months. Did you managed to get in contact with anyone from their staff (Andrea Riposati, Francesco Pennelli, Generoso Ianniciello, or Mattia Capulli) ? They are all members of that facebook group, if you're not a member yet, maybe it would be a good idea to join the group. So I assume you got so far exactly like me, the reports(1+2) and the 4 vcf's + 5 hidden files?
I totally agree with you that without the .bam and .fastq files, the way they advertised the product will be delivered, there is not that much of a use for the WGS test. I want to have my Ychr and Mtchr sections of my .bam analyzed by YFULL, but I can't slice a .bam and provide YFULL what they need, ahh and of course I have to realign to HG38 everything because... obviously the vcf's headers are pointing to my .bam that has been sequenced back mid April and aligned to the obsolete HG19. I am really curious ( I know I am an optimist :D ) when they'll finally provide my .bam and .fastq files, will they be as I requested: aligned to HG38 :-??
 
domogled said:
I am so sorry you are among the ones waiting for the HDD with the raw files all the way back since November. I understand that it is a cue line for the hdd orders, but the only reasonable explanation I see is the lab who sequenced your sample (BGi most probably) not delivering the hdd or simply deleted your raw files. it doesn't make any sense to keep on the cue someone for 7 months. Did you managed to get in contact with anyone from their staff (Andrea Riposati, Francesco Pennelli, Generoso Ianniciello, or Mattia Capulli) ? They are all members of that facebook group, if you're not a member yet, maybe it would be a good idea to join the group. So I assume you got so far exactly like me, the reports(1+2) and the 4 vcf's + 5 hidden files?
I totally agree with you that without the .bam and .fastq files, the way they advertised the product will be delivered, there is not that much of a use for the WGS test. I want to have my Ychr and Mtchr sections of my .bam analyzed by YFULL, but I can't slice a .bam and provide YFULL what they need, ahh and of course I have to realign to HG38 everything because... obviously the vcf's headers are pointing to my .bam that has been sequenced back mid April and aligned to the obsolete HG19. I am really curious ( I know I am an optimist :D ) when they'll finally provide my .bam and .fastq files, will they be as I requested: aligned to HG38 :-??
Click to expand...

I share your opinion about their problem with HDD delivery. Probably there is a problem with the lab that sequenced samples in first part of 2018. I know for one man who made order in April and he is still waiting for HDD. Dante Labs should openly says us what problem is and propose solution (refund or new test at their laboratory in Italy). I have contacted their customer servis several times, last time few days ago. Last time they reply on 30. May and prommised to check with bioinformatic team if there is any problem, no any information from them since then.
From Dante Labs I got only one SNP VCF and two reports. This VCF is almost useless, for example it has 3.102 chrY positions, in comparation Big Y700 VCF file has more than 180.000 chrY positions. I managed only to confirm my haplogroup and find one new SNP I share with a man tested on ftdna (thanks to hepl from adminstrators there).
Probably only way to have them do something is to start writing negative posts on Facebook.
I am member of the group Dante Labs Customers and suggest anyone interested in NGS and WGS to join, there are many interesting posts and discussions.
 
Domogled, Yfull recalculates "Hg19>Hg38" ... $15
Upgrade includes: reanalysis of all known SNPs; the search for new "private" SNPs; the search, analysis and verification of new (if they exist) candidates found (branch SNPs); re-evaluation of the quality of previously found "private" and known SNPs
Click to expand...
This is for existing customers that have uploaded results under HG19. There is a chance Yfull does the recalc. for new users for free.
And when you search for a certain snp in your results Yfull shows both positions (Hg19 and Hg38) even if you've decided not to upgrade.
 
Whaaaat? that sole vcf you've got is useless, it totally makes sense now they keep on delaying/stalling , something went wrong either in the sequencing process or with your sample. I have nearly 20k chrY positions in my raw.snp.vcf, if I add the ones from the raw.indel.vcf it goes around 23.9k
I knew my HG from previous tests, Dante's confirmed, and refined my previous results, it came with more SNP, my the analysis and comparison with other relevant kits being done by an enthusiast member of a group. Till he will get his BigY700 upgraded results, it appears that my VCF is the reference for comparisons in my tiny subclade.
As Andrea Riposati replied earlier today on the FB group it appears that all those members from "Dante Labs customers" FB group who requested HG38 realignment will get it for free ( of course once they will have the .bam's delivered on hard drives, I assume from China's sequncing lab).
I really think you should ask for a refund and see what offer they'd come with, if it was their fault, I just hope they will come to you with a good offer.


Vlad82 said:
I share your opinion about their problem with HDD delivery. Probably there is a problem with the lab that sequenced samples in first part of 2018. I know for one man who made order in April and he is still waiting for HDD. Dante Labs should openly says us what problem is and propose solution (refund or new test at their laboratory in Italy). I have contacted their customer servis several times, last time few days ago. Last time they reply on 30. May and prommised to check with bioinformatic team if there is any problem, no any information from them since then.
From Dante Labs I got only one SNP VCF and two reports. This VCF is almost useless, for example it has 3.102 chrY positions, in comparation Big Y700 VCF file has more than 180.000 chrY positions. I managed only to confirm my haplogroup and find one new SNP I share with a man tested on ftdna (thanks to hepl from adminstrators there).
Probably only way to have them do something is to start writing negative posts on Facebook.
I am member of the group Dante Labs Customers and suggest anyone interested in NGS and WGS to join, there are many interesting posts and discussions.
Click to expand...
 
That is great news, I was worried a bit about the realignement, yesterday I've found that YSEQ customers can ask for a realignment of a different /third party .bam file, of course not for free, but yet another option to have the .bam realigned. But if yfull is able to do it, that is a great alternative (and a lot cheaper than YSEQ :) )

td120 said:
Domogled, Yfull recalculates "Hg19>Hg38" ... $15

This is for existing customers that have uploaded results under HG19. There is a chance Yfull does the recalc. for new users for free.
And when you search for a certain snp in your results Yfull shows both positions (Hg19 and Hg38) even if you've decided not to upgrade.
Click to expand...
 
This company is soooo slow. I got my kit all right, and paid, and returned - but I still haven't seen any results and it's been three months. Ok - maybe acceptable time-wise, but I am even unsure if it's in their pipeline or not. THere's like zero information
 
Ten and a half months later.
I'd say patience pays dividends in the end, long wait but splendid sequencing quality

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127-46-GBases-2.png


So yeah BGI WGS sequencing quality in another league compared to the newly sequenced kits in Dante's lab in Italy, whose target is only 90GBases.
I'd say in the end you get what you pay for, though new kits get sequenced at 150bp while the BGI were done @100bp
 
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Dante labs is so ridiculously slow I agree. But I did get my data in the end and it looked good, matched SNPs with 23andme , results as expected etc
 
It used to be slow, the newly sequenced kits in their lab in Aquila Italy have a 6-8 weeks turnover. A colleague of mine ordered a sample on their Black Friday sale, and got its full results back on January the 2nd. He is already catching up with my sample's analysis on yfull which is great. The new kits however rarely get above 100GBases while the old ones had bigger coverage and double in size. I got a 92.8GB .bam file aligned to HG19 by Dante Labs, while my colleague's same HG19 by Dante Labs came around 43GB. I don't know if the size really matters but various tools reports a better coverage of my sequencing. However, Dante Labs changed in the past 3-4 months and whenever a good offer for their WGSx30 comes available I think it is the best consumer sequencing you can get for the money, last Black Friday with yfull discount code I think a kit came at 160 euros which is great price for any type of NGS.
 
As I mentioned in my previous post, a colleague of mine ordered a kit for Black Friday, used the yfull discount code and had it delivered in the UK by DHL 2 days later. Shipped it back 2 weeks later as he is a lazy sod :)) and got his results back 2nd of January. Everything smooth and sequencing quality exceeded my expectations getting around 108GBases. Sometimes is simply not meant to be, while some other times is just way beyond expectations... that's Dante Labs with goods and bads
 
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