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Miqui Rumba
09-30-2018, 09:39 AM
4 month! May 2, 2018 Dantelabs confirmed that my saliva sample have arrived. In August 1, I was worried and wrote a mail to the lab, they said me my kit was already processing and results may be to late August. Last week I could download my WGS snp.vcf from my account in Dantelabs web. Now I waiting hard disk with full raw data.

MacUalraig
10-02-2018, 02:00 PM
4 month! May 2, 2018 Dantelabs confirmed that my saliva sample have arrived. In August 1, I was worried and wrote a mail to the lab, they said me my kit was already processing and results may be to late August. Last week I could download my WGS snp.vcf from my account in Dantelabs web. Now I waiting hard disk with full raw data.

Did you get an interim message about passing QA? I got one 33 days after the sample reached the lab.

Giosta
10-03-2018, 12:40 PM
Dante received my kit yesterday (2 oct). Now I'm waiting ...

Miqui Rumba
10-03-2018, 09:39 PM
Last year, I bought WES kit in September and in November 11 I had my results already ( I paid 412€ by WES kit). I think this summer they have been overpowered by their prime day offerts and some clients like me have a delay to obtain results. I am not stressed, the fact of getting whole raw data in a hard disk is a real satisfaction, I can await.

Wed 5/2, 11:29 AM
You
Dante Labs: Kit received
Dear Customer,
We are pleased to confirm you we have received your sample. Our lab will start the DNA extraction as soon as possible.
Please do not hesitate to contact me if we may provide further assistance.
Best regards,

Dante Labs' Team

Geldius
10-08-2018, 10:24 PM
So how large is the BAM file they provide? Is it actually 100GB? That would be impossible to upload to YFull.

Ownstyler, I've got your PM, but can't reply.
Anthrogenica is saying: "Sorry Geldius you must have 10 posts in order to send PM's. Your current post count is 7."
Please, PM me your email :).

Petr
10-09-2018, 08:10 AM
I have files for 2 persons, one is 87 GB and the second 109 GB.

It is possible to separate chromosome Y data using samtools:


samtools view -b in.bam chrY > in_chrY.bam

KetoDude
10-19-2018, 02:58 AM
So far: They deliver with DHL and you get prepaid DHL labels to returns the samples. When samples kits are shipped you get DHL Waybill number so you can track the pack. It took just one day to get the kit (from Italy to Sweden) and one day to ship the kit back to Italy. My kits were marked as received the same day they were delivered. The WES kit status was updated after 11 days and I got a DNA-extraction report. I suppose that my sample is in sequencing now.
I ordered two WGS kits for my relatives in Russia and I was quite surprised that kits are send with DHL (it is not to big cities as St Petersburg and Moscow, but to rather distant smaller city). There were some additional documentation attached for the customs.


Did your relatives got their packaged sent directly from Italy to Russia with pre-paid DHL return labels?
No customs issues with receiving/sending samples? I know there are some kind of weird laws prohibiting sending biological samples in Russia.

My relatives are telling me that some people had to drive to another country, like Belarus, to send samples to services like 23andme. which is a major inconvenience if you live thousands miles from the border :-)

reignman
10-20-2018, 07:11 AM
I got an e-mail on 29. June that Dante Labs received my sample. On 16. October I got another e-mail that results are ready and VCF download link is available on my account. Processing time was about 15 weeks, it is pretty good.

MacUalraig
11-03-2018, 09:01 AM
They have had my sample since July 25th. I emailed them the other day for an update and was told it was being sequenced and I should have results by the end of November. I take that as a reference to the analysis reports inc vcf as its the BAM I am most focussed on.

zackdaugherty
11-06-2018, 09:01 PM
Just ordered my first 30x WGS for my father at Dante.

Things I'd like to do with the RAW data:
Generate a more complete atDNA kit for GEDmatch (low priority)
Package hg38 ChrY BAM for submission to Yfull (higher priority)
Package compatible mtDNA file for submission to Yfull (higher priority)
Generate a new VCF file for ChrY data for submission to the Y DNA Datawarehouse (higher priority)

- I understand that the downloadable VCF files are highly truncated and not ideal for much if I'm reading the comments here correctly. Potentially interesting ChrY variants could be missing from this data.

- That Dante BAM files are hg37 and not ideal for submission to Yfull (even though they can harvest ChrY and mtDNA data it still is in hg37).

All of this being said has anyone experienced using Dante Labs recommended App EVE to accomplish anything like the goals I outlined above? I can't post the link to EVE but you can view it by searching google for "Eve sequencing[dot]com".

MacUalraig
11-07-2018, 08:12 PM
I believe you can get it in hg19 or hg38 if you ask for it. That's based on some comments here on the technical thread and this on their website:

'We offer variant calling against hg19 (GRCh37) or hg38 (GRCh38), depending on the customers' needs.'

There have been YFull submissions in both. If someone asked for hg38 recently and was declined please correct me.

Miqui Rumba
11-08-2018, 05:46 PM
Gedmatch Genesis rejected 5 times my Dantelabs WGS snp.VCF uploading. Finally, I worked with Beagle 4.1 (without map, default settings: 1 cM/1 Mb) to generate a lighter VCF (only 18 Mb compressed by bgzip). New kit NY6801335 matches perfectly to my 23andme kit and my father's GFG. Only my Gencove imputed VCF shares less percentage, about 98%

reignman
11-08-2018, 07:30 PM
Gedmatch Genesis rejected 5 times my Dantelabs WGS snp.VCF uploading. Finally, I worked with Beagle 4.1 (without map, default settings: 1 cM/1 Mb) to generate a lighter VCF (only 18 Mb compressed by bgzip). New kit NY6801335 matches perfectly to my 23andme kit and my father's GFG. Only my Gencove imputed VCF shares less percentage, about 98%

Gedmatch Genesis accepts only hg19 while my vcf is in hg38, is there any way to convert it?

Miqui Rumba
11-09-2018, 12:15 AM
Yes, you can convert human references with liftover tool, it is free in UCSC and Ensembl webs though I prefer usegalaxy.org platform because I can filter and normalize SNPs with another programs (picard tools, bcftools). However, we must collaborate to make an standard genealogic pattern, collecting only SNPs wich accepts Gedmatch genesis and Eurogenes calculators. Genesis processed 1.8M SNPs from 3.5M total SNPs and selected only about 500,000 SNPs. When I ran Eurogenes k36 calculator in chromosome view I've seen that only chroms 1,2 and 3 have thousands of SNPs selected, the rest 1 o 0 SNPs (impossible to get results). MDLP calculators run better results for WGS kits.

BroderTuck
11-09-2018, 07:36 AM
I read that YSEQ provides a special vcf file with their WGS test, a file that includes the SNPs used in versions 2-5 of the 23andme chips. That should give good matching to all autosomal products except maybe the new Ancestry V2 test.

reignman
11-10-2018, 03:34 PM
Yes, you can convert human references with liftover tool, it is free in UCSC and Ensembl webs though I prefer usegalaxy.org platform because I can filter and normalize SNPs with another programs (picard tools, bcftools). However, we must collaborate to make an standard genealogic pattern, collecting only SNPs wich accepts Gedmatch genesis and Eurogenes calculators. Genesis processed 1.8M SNPs from 3.5M total SNPs and selected only about 500,000 SNPs. When I ran Eurogenes k36 calculator in chromosome view I've seen that only chroms 1,2 and 3 have thousands of SNPs selected, the rest 1 o 0 SNPs (impossible to get results). MDLP calculators run better results for WGS kits.

Thank you! Platform usegalaxy.org looks nice, I am going to learn how to use it. Unfortunately, I am new in this.

MacUalraig
11-18-2018, 10:01 AM
Dante Labs Black Friday sale is now on, 169 Euros for a WGS test!


My Full DNA: Whole Genome Sequencing with mtDNA
€169.00 EUR €850.00 EUR You save €681.00 EUR

https://www.dantelabs.com/products/whole-genome-sequencing

lnight
11-18-2018, 10:27 AM
Dante Labs Black Friday sale is now on, 169 Euros for a WGS test!

Question though, how much better is their GenomeZ version? I was hoping that would be taken down a couple hundred dollars but it's never on sale. I'm fairly new to sequencing and trying to learn technical terms. So far it looks like that test has higher resolution exome sequencing? Is there something I'm missing? There is a huge price gap between the two tests, even when not on sale. Dante Labs also said they were working on long read sequencing 7 days ago. If that is even better, would it be worth waiting for?

reignman
11-18-2018, 11:00 AM
Dante Labs Black Friday sale is now on, 169 Euros for a WGS test!


My Full DNA: Whole Genome Sequencing with mtDNA
€169.00 EUR €850.00 EUR You save €681.00 EUR



At this price, we should add an additional fee €59 for fard disc that contains FASTQ and BAM files.

So for people who wish Yfull analysis price is actually 169+59=228€
Anyway, I think this is currently the cheaper WGS.

MacUalraig
11-18-2018, 02:51 PM
Question though, how much better is their GenomeZ version? I was hoping that would be taken down a couple hundred dollars but it's never on sale. I'm fairly new to sequencing and trying to learn technical terms. So far it looks like that test has higher resolution exome sequencing? Is there something I'm missing? There is a huge price gap between the two tests, even when not on sale. Dante Labs also said they were working on long read sequencing 7 days ago. If that is even better, would it be worth waiting for?

Yes the Z version does high read sequencing of the exome at 130x then 30x for the rest of the genome. Depends on your budget and how interested you are in the autosomal data (eg health related information). If you are only interested in a cheap route to a Y sequencing stick with the cheaper version since it will be the same coverage, except of course for a sprinkling of genes on the Y which would be covered at greater depth.

DebbieK
11-18-2018, 03:25 PM
I wrote a blog post here with further details:

https://cruwys.blogspot.com/2018/11/a-30x-whole-genome-sequence-from-dante.html

reignman
11-18-2018, 03:47 PM
I wrote a blog post here with further details:



Excellent blog post Debbie!
There is one mistake about price for WGS 30x at Yseq, it $740 (regular price for 15x) + $600 (for 30x) + $100 (sanger confirmation, optional).

MacUalraig
11-18-2018, 04:10 PM
I wrote a blog post here with further details:

https://cruwys.blogspot.com/2018/11/a-30x-whole-genome-sequence-from-dante.html

YFull have already processed Dante BAM files and their service includes SNP matching with messaging (and extracted STR matching too if you really want them) not just Y-SNP reports.

They currently list 11 different accepted sources for BAM files on their order page at

https://www.yfull.com/order/

DebbieK
11-18-2018, 05:12 PM
Thanks MacUalraig and reignman. I've now corrected the blog post with that new information. I didn't see the plus sign on the YSEQ website when I was writing the blog post late last night!

Cassoulet
11-19-2018, 10:21 PM
30x is enough ?

I also heard that soon illumina will provide a chip that is capable to sequence your whole genome for 100$ certainly to companies like 23andme. https://twitter.com/coregenomics/status/1058790189752049664

so what do I do ? order now and receive it in 5-6 months (since dante lab never respect their deadline according to the fb page) or wait for 1 or 2 years and get WGS from big company or better quality anyhow ?

they do not seems very professional https://www.cnbc.com/2018/06/15/dant...customers.html even if it's the transporter fault it seems.

poi
11-20-2018, 01:55 AM
30x is enough ?

I also heard that soon illumina will provide a chip that is capable to sequence your whole genome for 100$ certainly to companies like 23andme. https://twitter.com/coregenomics/status/1058790189752049664

so what do I do ? order now and receive it in 5-6 months (since dante lab never respect their deadline according to the fb page) or wait for 1 or 2 years and get WGS from big company or better quality anyhow ?

they do not seems very professional https://www.cnbc.com/2018/06/15/dant...customers.html even if it's the transporter fault it seems.

I do not think 23andme is going to offer WGS for $100 in the next few years when they continue to sell the limited 600k SNPs for $99 for 11 months of the year. Looks to me that their base customers are just interested in their (last 200 years of) ancestry, not genetics.

Unless something drastic happens soon, they will continue to milk the old chip. And perhaps add WGS for $1000 (with $500 promo deals once a while).

cercle
11-22-2018, 09:09 AM
I received e-mail 28 of september saying my DNA was succesfully extracted and ready for sequencing. I can speculate getting my VCF during December.

Erikl86
11-23-2018, 02:27 PM
I just purchased the 169 euro deal.

Will share my results as soon as they are available.

poi
11-23-2018, 07:20 PM
I bought one as well. Pretty good deal... the data will be VCF but we can order BAM in a drive separately.

Erikl86
11-23-2018, 07:52 PM
I bought one as well. Pretty good deal... the data will be VCF but we can order BAM in a drive separately.

From what I gather, the VCF works fine in Genesis.

poi
11-23-2018, 10:33 PM
From what I gather, the VCF works fine in Genesis.

I have uploaded VCFs before(linked from DNAland I think) and they work fine for Gedmatch. But for full control of the data, BAM would be the greatest and we can do whatever with the true raw. The only limit would then be the present tech of 30x, while future(in a few years), it could be 100x. Don't ask me what that means, just 100x sounds better than 30x... but for $200, if DanteLab delivers, then it is a damn good deal.

Miqui Rumba
11-23-2018, 11:45 PM
I have uploaded VCFs before(linked from DNAland I think) and they work fine for Gedmatch. But for full control of the data, BAM would be the greatest and we can do whatever with the true raw. The only limit would then be the present tech of 30x, while future(in a few years), it could be 100x. Don't ask me what that means, just 100x sounds better than 30x... but for $200, if DanteLab delivers, then it is a damn good deal.

I have a Dantelabs WES x100 kit and another kit WGS x30. If you are dreaming of every position in your genomes may be read 100 times, please, wake up. In my Whole exome sequencing kit (x100 readings AVERAGE) almost 20% tested loci have very low pass or less than x10 readings. Some regions of most important genes have x300 readings although they are a little percentage. I think Dantelabs gives better results in VCF with WGS x30 than in WES x100, in fact, they don't sell WES alone anymore (only both WGS in Z pack).
I have a Gencove imputed VCF maden from my 23andme v4 raw data (Gedmatch Genesis kit GN9840488) with more than 30,000 Snpedia genos in Promethease's report and my Dantelabs WGS x30 snp.VCF (Gedmatch Genesis kit NY6801335) with 19,000 Snpedia genos in Promethease's though all dubious. Dr. Joe Pickrell Gencove imputation gessed my rare blood Lewis negative, I spent more than 800 in Dantelabs kits to confirm this speculation because of one SNP in 23andme raw data looks like Lewis positive.
Comparing Kit GN9840488 (*GENCOVE IMPUTED VCF) [Gencove] and NY6801335 (mrvWGS Beagle) [-]

Segment threshold size will be adjusted dynamically between 200 and 400 SNPs
Minimum segment cM to be included in total = 7.0 cM
Mismatch-bunching Limit will be adjusted dynamically to 60 percent of the segment threshold size for any given segment.
Largest segment = 146.4 cM

Total Half-Match segments (HIR) = 3518.9 cM (98.201 Pct)
Estimated number of generations to MRCA = 1.0

59 shared segments found for this comparison.

286837 SNPs used for this comparison.

98.562 Pct SNPs are full identical

bmoney
12-01-2018, 04:01 AM
I bought one as well. Pretty good deal... the data will be VCF but we can order BAM in a drive separately.

Give us an update when you get it!

dufresda
12-01-2018, 04:51 AM
Anyone recieve sample back from US? If so what date and time ?
I know its a European company answering emails 3-5am EST . curious if results can be recieved during weekends or anytime during the day or are there cutoffs

poi
12-01-2018, 08:23 AM
Anyone recieve sample back from US? If so what date and time ?
I know its a European company answering emails 3-5am EST . curious if results can be recieved during weekends or anytime during the day or are there cutoffs

I have not received it yet.

MacUalraig
12-02-2018, 10:14 AM
Their email of Oct 30 told me 'You are expected to receive the final results by the end of November. ' However, in reality... :-(

cercle
12-03-2018, 09:07 PM
I actually got my VCF tonight !

ordered 8/17/2018
Success DNA grade A extraction 9/28/2018
Vcf ready to download 12/3/2018

dufresda
12-04-2018, 12:19 AM
Oh thats great news ! Although my DNA was extracted a month before yours :(... What time? Timezone?

cercle
12-04-2018, 06:33 AM
Oh thats great news ! Although my DNA was extracted a month before yours :(... What time? Timezone?

Sample was sent to L'Aquila, Italia.

dufresda
12-04-2018, 11:38 AM
I know people have gotten there samples back , back but for me it seems like a dream or scam. Many people said they recieve emails with updates. I have not aside fron dna extraction, I would have to ask and the deadline has been missed and the antcipated result availability communicated was also missed twice :( end of October and end of November. I selected this company as a catch all WGS as opposed to the popular Family Tree DNA Big Y , anyway it's a smaller company lets see . will be receiving raw dna to compare against raw DNA received from other companies and post comparison

cercle
12-04-2018, 03:28 PM
I share your frustration. Looking across many comments, it looks like some people had problems getting results in due time without clear explanations. Maybe I fell in a lucky batch and/or managment went better when I sent my sample !

MacUalraig
12-04-2018, 04:00 PM
I actually got my VCF tonight !

ordered 8/17/2018
Success DNA grade A extraction 9/28/2018
Vcf ready to download 12/3/2018

Lucky! You ordered a month after I did. I have now had an apologetic email but it didn't offer an ETA.

cercle
12-04-2018, 05:09 PM
Hope you get yours soon. I have not received yet an e-mail saying my results are ready.

I had to copy paste the whole link in my browser to start download because "page not found" when I clicked on it.

27497

No medical report to download either yet.
My experience is overall positive. File is easy to browse with sequencing data viewer app with filters and links to clinvar.

27498

Also compatible with enlis genome, very convenient for somebody like me not at ease with such files.

Now I have knowledge of dozens of variants well under 1% reported possibly damaging by clinvar and almost the same numbers of "uncertain significance" in very important genes about neuroligical or cardiovascular disease/conditions. WOW ! I hate my curiousity in that moment...

mixmaxdp
12-10-2018, 08:56 AM
another datapoint to the thread:
after reading all the contradicting not-so-happy experiences with DanteLabs I finally bit the bullet and have purchased their $199/EUR169 30x WGS kit during BF promo too
(+ friend of mine has bought it as well).

I do realize that actual results will probably come in in about 6 months or so, so don't keep my hopes for quick turnaround too high
Initial email stated that order updates expected after Dec 03, finally received tracking number 4 days ago but it still shows up as "pending info from carrier" and tracking# from first glance does not look like it is DHL or fedex, more like ordinary international snail mail. Will post updates on how it goes.

dufresda
12-10-2018, 09:25 AM
Still nothing day 124, of the advertised 55 days turnaround. Company no longer responds to me sent a mail to CEO no response. I bought my kit for 350 and will be upfront and honest and say I am starting to regret it , they were backlogged since beginning of the year . countless sales not catching up removing reviews and peoducta from Amazon is not a good impression . I hope the company can turn around . but customer impression seems horrible aside from a small number getting results and bloggers . it was between this company 350 and FTDNA for 450 you do get more for the 350 or 200 now but birthpangs seem to be overbearing. And the responae ia just wait ir will be worth it but this is not correct attitude . these need to get fixed , thia is why companies halt peocesses to make sure they get back order quality is one thing customer impression is another if all customers wait half a year for a turn around 55 days some wont mind but this overall is very bitter and with prices of rep companies coming down it will be diff in the future with results coming every 6 months

MacUalraig
12-10-2018, 12:24 PM
Fair enough comments except that one of those is a WGS and the one you compared it with isn't.

If people want a WGS done quickly (relatively speaking) and can afford the higher budget the YSEQ WGS is probably the way to go right now. They have turned around kits they already had in 4 weeks - if its a new kit you need to allow for DNA extraction and QA which is another 2-3w.

pmokeefe
12-12-2018, 04:29 PM
We received a kit from Dante Labs at our United States address, made the sample, and using the shipping label supplied, shipped it back to Dante Labs in Italy. But the shipping status was "Unable to deliver shipment, returned to shipper"
When we checked with Fedex, they said the shipment was rejected by Italian Customs. I sent emails to Dante Labs about this problem on Nov 30 and Dec 4th and received no response (it is now Dec 12th). In the meantime, the kit was returned back to us by the shipper. Has anyone else in the United States had this problem? Is there a United States address for Dante Labs so we ship the kit there instead of back to Italy?

poi
12-12-2018, 05:31 PM
We received a kit from Dante Labs at our United States address, made the sample, and using the shipping label supplied, shipped it back to Dante Labs in Italy. But the shipping status was "Unable to deliver shipment, returned to shipper"
When we checked with Fedex, they said the shipment was rejected by Italian Customs. I sent emails to Dante Labs about this problem on Nov 30 and Dec 4th and received no response (it is now Dec 12th). In the meantime, the kit was returned back to us by the shipper. Has anyone else in the United States had this problem? Is there a United States address for Dante Labs so we ship the kit there instead of back to Italy?

That isn't good. I have not yet received mine (in the US).

pmokeefe
12-12-2018, 07:27 PM
I live part-time in Italy and I had previously ordered kits from Dante while I was there and was happy with those results so far.
But recently I ordered kits for family members in the United States, they arrived in a reasonable time, less than two weeks from the order, I believe.
How long have you been waiting for yours?
But the first one got sent back from Italy due to Customs, I'm holding the others until this gets resolved.
Hopefully they also have a U.S. return address and I was mistakenly given the Italian return address because of my previous orders from Italy.
I would like to hear the recent experience from other U.S. customers.

Geldius
12-12-2018, 08:53 PM
I would like to ask you, if somebody of you successfully aligned (on PC) Dante's FASTQs to SAM/BAM hg38 ?

MacUalraig
12-13-2018, 03:08 PM
I would like to ask you, if somebody of you successfully aligned (on PC) Dante's FASTQs to SAM/BAM hg38 ?

I believe one or two have been doing this if you check out the Dante technical thread, just to keep this one a bit more non-technical...

https://anthrogenica.com/showthread.php?13642-Dante-Labs-WES-WGS-Sequencing-Technical

Tonev
12-16-2018, 07:01 PM
Hello, being stuck intermediarily (I hope) between link to .VCF file (in week 16) and receiving a HDD with other raw data incl. .BAM, .FASTQ and FASTA, I am wondering:
1. how much time can it take receiving the HDD, having in mind that instead of sending the HDD right afterwards, Dante Labs pretended quite surprisingly (diplomatically put) that I must have explicitly ordered such sending for a second time after the order and independently of their initial package offer;
2. what could be worth trying with the .VCF file while waiting the HDD;
3. did Dante Labs ever send .bam/otehr file as cloud based links.

pmokeefe
12-17-2018, 03:48 PM
As a followup, today I did receive return shipping labels for my United States address kits to a return address in America. Hopefully that will work this time! I would like to hear the experiences of any other American customers of Dante Labs.

dufresda
12-17-2018, 10:01 PM
I am from US , kit recieved end of July , extracted end of August , still waiting I was told end of October then end of November now end of December. The wait is seriously a problem, they say backlogged due to unexpected amount of kit purchases yet they keep lowering prices and discounts on top of backlog . I would think they need to get ahead on what they have first ? Also this cannot be unexpected it's essential caused by content lower process and there are no responses publicly to address backlog just silence on the issue while welcoming new kits

Youtube review took 8 weeks apparently not sure how they prioritize maybe review bloggers and hospitals ?but it seems people getting theirs alot sooner is possible. I'm at 5 and half months a little more than double the YouTuber's time frame

https://youtu.be/rP42QBhgmHo

Miqui Rumba
12-17-2018, 11:39 PM
Good news for WGS kits in Gedmatch Genesis: if you had another parent/son kit kit (genealogical as FTDSNA, Ancestry, 23andme...) and you make phasing with your Dantelabs WGS kit then surprisingly phased kits shows real segments shared with another WGS kits! you can check my parents phaseing kits NY6801335M1 (half DNA from my mother) and NY6801335P1 (my father's Genes for Good imputation converted back to 23andme v3 with Wilhem's HO DNA Studio). My Gencove's imputed VCF kits are better after phasing also.

poi
12-18-2018, 12:08 AM
Just dropped off my kit at the local USPS collection center. I purchased during the Black Friday sales event. Hopefully, it won't take 6 months before the results are ready.

pmokeefe
12-19-2018, 02:18 AM
I ordered my Dante Labs test in March 2018, received the results at the end of July. My Dante Labs Test Results are now available to the public. This Google Drive folder contains test results from various labs, the Dante Labs results are in subfolder 15001710504417A.
https://drive.google.com/drive/folders/1_x7ZtSenJNUyb9nsq0hcNbyizx1a39F3?usp=sharing
Included are the vcf,gvcf,bam and fastq files as well as their Wellness and Longevity report. Please feel free to take a look at those if you're considering taking the test or are waiting for your results and are wondering what you might get back - or for any other purpose.
Subsequently I have ordered six other kits from them, for family members and extra coverage for myself. I have not received any of those results yet as the orders were fairly recent.

MacUalraig
12-19-2018, 08:34 AM
I am from US , kit recieved end of July , extracted end of August , still waiting I was told end of October then end of November now end of December. The wait is seriously a problem, they say backlogged due to unexpected amount of kit purchases yet they keep lowering prices and discounts on top of backlog . I would think they need to get ahead on what they have first ? Also this cannot be unexpected it's essential caused by content lower process and there are no responses publicly to address backlog just silence on the issue while welcoming new kits

Youtube review took 8 weeks apparently not sure how they prioritize maybe review bloggers and hospitals ?but it seems people getting theirs alot sooner is possible. I'm at 5 and half months a little more than double the YouTuber's time frame

https://youtu.be/rP42QBhgmHo

Not seen that before, thanks although not quite sure why we need a vid of him producing saliva...
Has to be said that as he got his free his delivery timescale was probably better than what Joe Public gets (as we already knew).

Particularly intriguing is his subsequent claim that he got his 'raw data' in 8w too but no further details. Maybe he is referring to his VCF rather than his BAM file?

Giosta
12-19-2018, 08:54 PM
I ordered my Dante Labs test in March 2018, received the results at the end of July. My Dante Labs Test Results are now available to the public. This Google Drive folder contains test results from various labs, the Dante Labs results are in subfolder

Hi

Who uploaded the data to Google Drive, you or Dante Labs ?

Are you going to upload the data to YFull ? Can YFull download the data from Google Drive ? What files they want chrM.bam and chrY.bam ?

Many questions but my Dante results are soon ready and I'd like to know something before ..

pmokeefe
12-19-2018, 11:24 PM
Hi

Who uploaded the data to Google Drive, you or Dante Labs ?

Are you going to upload the data to YFull ? Can YFull download the data from Google Drive ? What files they want chrM.bam and chrY.bam ?

Many questions but my Dante results are soon ready and I'd like to know something before ..

I uploaded the data myself to my own Google Drive account. I believe I received the vcf file first via an AWS link sent by Dante Labs. Later they sent me a hard drive with the bam and fastq files. That was in July, so I'm not sure if the current procedure is the same.

I did upload to YFull (YF14620). That was back in August, I don't recall the exact process, sorry.

poi
12-23-2018, 06:24 PM
This is strange. The kit was expected to be delivered yesterday, but I got the alert from USPS tracking.

SATURDAY
22
DECEMBER
2018
by
8:00pm
Alert
December 22, 2018 at 9:02 am

Delivery Attempted - No Access to Delivery Location

DRAPER, UT 84020

Hopefully they retry again. And hopefully the address exists. I simply used the pre-printed label.

pmokeefe
12-23-2018, 10:15 PM
This is strange. The kit was expected to be delivered yesterday, but I got the alert from USPS tracking.

SATURDAY
22
DECEMBER
2018
by
8:00pm
Alert
December 22, 2018 at 9:02 am

Delivery Attempted - No Access to Delivery Location

DRAPER, UT 84020

Hopefully they retry again. And hopefully the address exists. I simply used the pre-printed label.

I had a kit that was reported delivered to their Draper UT address by Fedex on 12/20. I hope yours gets through, please keep us posted.

dufresda
12-26-2018, 05:05 PM
Just checking in, still nothing I was told end of December, Third target .....anyone get Christmas surprise ??

poi
12-26-2018, 05:23 PM
I had a kit that was reported delivered to their Draper UT address by Fedex on 12/20. I hope yours gets through, please keep us posted.

USPS has not updated its tracking, so I have emailed DanteLabs to see what could be going on.

dufresda
12-26-2018, 08:17 PM
Have you tried contacting USPS?

poi
12-27-2018, 05:41 AM
Finally, USPS delivered. I think they waited after the holidays to re-try. So, I assume DanteLabs will have the sample and there is going to be at least a few months of waiting.



Your item was delivered to the garage or an alternate location at the address at 3:04 pm on December 26, 2018 in DRAPER, UT 84020.

Status
Delivered
December 26, 2018 at 3:04 pm

Delivered, Garage or Other Location at Address

DRAPER, UT 84020

Erikl86
01-02-2019, 10:39 AM
I just got my kit, gonna spit and send it this Friday.

KCW
01-02-2019, 06:48 PM
My two kits passed quality control a few days ago.

Petr
01-04-2019, 12:45 AM
One of my Dante WGS tests has just 2 FASTQ files, but the second has many of them. Does anybody know how to convert them to one unmapped BAM file?
I have the following files for one sample:
CL100060446_L01_525_1.fq.gz
CL100060446_L01_525_2.fq.gz
CL100060446_L01_526_1.fq.gz
CL100060446_L01_526_2.fq.gz
CL100060446_L01_527_1.fq.gz
CL100060446_L01_527_2.fq.gz
CL100060446_L01_528_1.fq.gz
CL100060446_L01_528_2.fq.gz
CL100060446_L01_529_1.fq.gz
CL100060446_L01_529_2.fq.gz
CL100060446_L01_530_1.fq.gz
CL100060446_L01_530_2.fq.gz
CL100060446_L01_531_1.fq.gz
CL100060446_L01_531_2.fq.gz
CL100060446_L01_532_1.fq.gz
CL100060446_L01_532_2.fq.gz

dufresda
01-04-2019, 06:51 AM
Side question, You just got your results ?

Petr
01-04-2019, 08:05 AM
I got the results long time ago.

1st kit:
Delivered (tracking): 2017-10-13
Sample received: 2017-10-18
DNA Extracted: 2017-10-31
Results ready: 2018-01-28
Flash drive shipped: 2018-03-21
HD shipped: 2018-06-27 (with corrected FASTQ files)

2nd kit:
Delivered (tracking): 2017-12-13
Sample received: 2017-12-15
DNA Extracted: 2018-01-05
Results ready: 2018-04-17
HD shipped: 2018-06-12

Now I sent 3rd to 7th kit:
Delivered (tracking): 2018-01-03

and I'm curious to see what will be the turnaround time this year.

dufresda
01-04-2019, 02:55 PM
Ok,

do you mean 2019-01-03? because I would have expected if you sent 2018-01-03 it would have already had results, that's is my guess and hope that would make it little more than a year now which is the highest turn around thus far.

J Man
01-04-2019, 04:36 PM
My kit was received by them a few weeks ago. I am excited to receive my results.

Erikl86
01-04-2019, 09:10 PM
I have a problem - for some reason my UPS label expired - anyone know where to send them the kit in such a case?

pmokeefe
01-04-2019, 10:09 PM
I have a problem - for some reason my UPS label expired - anyone know where to send them the kit in such a case?

When I emailed them at [email protected] they sent me new prepaid shipping labels. They don't always reply in a timely fashion, but when they do reply they have always been quite helpful.

poi
01-05-2019, 04:55 AM
I registered my kit on their website as soon as I sent it... USPS delivered it on 12/26, but the website status is still showing "Waiting confirmation from Dante Labs". I don't know when that message will change.

traject
01-05-2019, 04:58 AM
I registered my kit on their website as soon as I sent it... USPS delivered it on 12/26, but the website status is still showing "Waiting confirmation from Dante Labs". I don't know when that message will change.

I think they're backlogged;my package was only recently updated to received but it was "Waiting for confirmation" for a while.

poi
01-05-2019, 05:00 AM
I think they're backlogged;my package was only recently updated to received.

I bet they'd be backlogged when they sold WGS 30x for $199... I'm kicking myself for not ordering 5 kits. I knew I would regret not ordering more. But put it off.

Petr
01-05-2019, 11:01 AM
Ok,

do you mean 2019-01-03? because I would have expected if you sent 2018-01-03 it would have already had results, that's is my guess and hope that would make it little more than a year now which is the highest turn around thus far.

Yes, it was 2019-01-03, sorry.

Tonev
01-05-2019, 11:57 AM
Petr, why is that two months time between "results ready" and "HD shipped"???That makes no sence.... Especially for cases like mine, in which the price includes HDD shipment of BAM file...
Link to my VCF file was finally uploaded in the web site of Dante on 9th of December 2018. Upon my Question about the other raw data (Bam, fastq, fasta), Dante Labs replied that if I need the pre-payed raw data cited, they can add me to their HDD shipping queue, which sounded so odd having in mind that it is integral part of the price...
And if their time frame with your two kits are typical for Dante Labs, I have to wait until February 2019 for the HDD with BAM..??

reignman
01-05-2019, 05:31 PM
Petr, why is that two months time between "results ready" and "HD shipped"???That makes no sence.... Especially for cases like mine, in which the price includes HDD shipment of BAM file...
Link to my VCF file was finally uploaded in the web site of Dante on 9th of December 2018. Upon my Question about the other raw data (Bam, fastq, fasta), Dante Labs replied that if I need the pre-payed raw data cited, they can add me to their HDD shipping queue, which sounded so odd having in mind that it is integral part of the price...
And if their time frame with your two kits are typical for Dante Labs, I have to wait until February 2019 for the HDD with BAM..??

I have been waiting for the HDD with BAM and FASTA since 2th November 2018. So it surelly takes 2 months or more.
Firstly I had supposed they would sent it imediatelly without any additional request, about two week after received VCF file I contacted customer support and they added me in the queue. Good news is that customer support person said they can also provide download link for third party analysis.

yhamm
01-06-2019, 09:53 AM
Ich have been added to the HDD Queue on September 4th 2018 and still have not received it. Kit was ordered in March 2018 and results were ready by end of August...

Tonev
01-06-2019, 12:34 PM
I have been waiting for the HDD with BAM and FASTA since 2th November 2018. So it surelly takes 2 months or more.
Firstly I had supposed they would sent it imediatelly without any additional request, about two week after received VCF file I contacted customer support and they added me in the queue. Good news is that customer support person said they can also provide download link for third party analysis.

Yes, but thus it turns to be even more ridiculous in terms of user friendliness and communication.
1. Concerning their timeframe, the only thing their user knows is the preliminary info about 10-12 weeks processing period for getting the results. And that period actually turns to be at least 3 weeks more.
2. No preliminary or follow-up information about any other queues (hdd, etc.), any other user actions, required by Dante but unknown to users (like explicit order for adding to hdd queue), time for delivery (average/maximum), alternative/parallel ways of delivery (hdd / link to to all raw data / both)
Yes, there are cost issues (hdd vs web hosting), there are privacy issues of the access to raw data (hdd vs web link)
But we expect fair communication from the servicee provider so that we would make our choices and decisions with eyes open....

Helves
01-06-2019, 02:29 PM
How well does the raw data from Dante labs work with third party websites like say, Gedmatch?

Tonev
01-06-2019, 06:36 PM
How well does the raw data from Dante labs work with third party websites like say, Gedmatch?

As I am still having only the VCF file with unique variants (waiting for all other raw data from DanteLabs), I have tried it in Gedmatch Genesis. It was accepted normally and provides access to all available comparisons. The One-to-many comparison returns my FTDNA autosomal file as number 18 in the results page. One to one comparison returns highest possible rsults among all others: 99,995 pct SNPs full identical.

Helves
01-06-2019, 06:54 PM
As I am still having only the VCF file with unique variants (waiting for all other raw data from DanteLabs), I have tried it in Gedmatch Genesis. It was accepted normally and provides access to all available comparisons. The One-to-many comparison returns my FTDNA autosomal file as number 18 in the results page. One to one comparison returns highest possible rsults among all others: 99,995 pct SNPs full identical.
Thanks.
You don't mind sharing the difference between your ftdna kit and the Dante Labs kit in one of the calcs on Gedmatch?

Tonev
01-06-2019, 07:04 PM
Thanks.
You don't mind sharing the difference between your ftdna kit and the Dante Labs kit in one of the calcs on Gedmatch?

You mean like that?


Largest segment = 131.9 cM

Total Half-Match segments (HIR) = 3531.4 cM (98.469 Pct)
Estimated number of generations to MRCA = 1.0

58 shared segments found for this comparison.

311964 SNPs used for this comparison.

99.952 Pct SNPs are full identical

Comparison took 0.229 seconds.
CPU time used: 0.040 cpu seconds.

Ownstyler
01-06-2019, 08:50 PM
As I am still having only the VCF file with unique variants (waiting for all other raw data from DanteLabs), I have tried it in Gedmatch Genesis. It was accepted normally and provides access to all available comparisons. The One-to-many comparison returns my FTDNA autosomal file as number 18 in the results page. One to one comparison returns highest possible rsults among all others: 99,995 pct SNPs full identical.

How did you receive unique variants? Aren't all the variants in the VCF file unnamed? How can you identify the unique ones?

reignman
01-06-2019, 10:09 PM
As I am still having only the VCF file with unique variants (waiting for all other raw data from DanteLabs), I have tried it in Gedmatch Genesis. It was accepted normally and provides access to all available comparisons. The One-to-many comparison returns my FTDNA autosomal file as number 18 in the results page. One to one comparison returns highest possible rsults among all others: 99,995 pct SNPs full identical.

Did you convert VCF to GRCh37/hg19 before upload to Gedmatch Genesis?

Helves
01-06-2019, 10:10 PM
You mean like that?


Largest segment = 131.9 cM

Total Half-Match segments (HIR) = 3531.4 cM (98.469 Pct)
Estimated number of generations to MRCA = 1.0

58 shared segments found for this comparison.

311964 SNPs used for this comparison.

99.952 Pct SNPs are full identical

Comparison took 0.229 seconds.
CPU time used: 0.040 cpu seconds.

I meant more like the results you are getting with the various calculators on Gedmatch, like say Eurogenes K13 or Dodecad K12b. Is the difference between your ftdna kit and the one from Dante Labs big?

Tonev
01-07-2019, 05:08 PM
How did you receive unique variants? Aren't all the variants in the VCF file unnamed? How can you identify the unique ones?

If I understand you correctly, I did a simple MS Access query with two tables: 1. the Y-DNA fraction from the VCF + 2. the latest ISOGG Y-DNA index file. Common column: Position (Build 37 Number). That's what I have "invented" for my manual researches while waiting the BAM (is it really two months???) so that could submit it to YFULL. I shared some details about this exercise plus another one (comparing with ancient G2A) in the Facebook group "Haplogroup G"

Tonev
01-07-2019, 05:08 PM
Did you convert VCF to GRCh37/hg19 before upload to Gedmatch Genesis?

The VCF itself is GRCh37/hg19

Tonev
01-07-2019, 05:24 PM
I meant more like the results you are getting with the various calculators on Gedmatch, like say Eurogenes K13 or Dodecad K12b. Is the difference between your ftdna kit and the one from Dante Labs big?
Here is the One-to-one comparison.
28196

Ownstyler
01-07-2019, 06:31 PM
Has anyone been communicating with Dante Labs recently? I have received no responses from them since Dec 22nd.

dufresda
01-07-2019, 07:20 PM
Same no response, they seem to get selectivly responses on twitter

Tonev
01-07-2019, 08:02 PM
No response neither by e-mail, nor in FB since 20th Dec.

ssamlal
01-07-2019, 10:43 PM
I registered my kit on their website as soon as I sent it... USPS delivered it on 12/26, but the website status is still showing "Waiting confirmation from Dante Labs". I don't know when that message will change.

USPS delivered my kit on 12/26 as well. I just received an email from Dante Labs (today) confirming receipt. I think yours will be updated soon.

For those of us in Canada, the prepaid envelope also works (i.e. Canada Post will not charge to forward on to USPS, and you can place in any post box).

poi
01-07-2019, 11:16 PM
USPS delivered my kit on 12/26 as well. I just received an email from Dante Labs (today) confirming receipt. I think yours will be updated soon.

For those of us in Canada, the prepaid envelope also works (i.e. Canada Post will not charge to forward on to USPS, and you can place in any post box).

You're right. They updated mine as well.

Ric69
01-08-2019, 07:18 PM
From Petr:


"Now I sent 3rd to 7th kit:
Delivered (tracking): 2018-01-03"

Did you mean 2019-01-03 ?

I would be very curious if ANYONE has received results from Dante labs in the last several months. I see no apparent activity from them in terms of processing the DNA; just marketing stuff and generic excuses. (???)

reignman
01-08-2019, 07:39 PM
The VCF itself is GRCh37/hg19

All my Y-DNA SNPs are HG38 positions.

dufresda
01-08-2019, 07:39 PM
It seems that after batches submitted around March 2018 have been delivered late 2018 , none others reported that I have seen who have submitted after that date recieved that I know of with the exception of bloggers etc...

J Man
01-08-2019, 08:21 PM
My kit was updated to "received" yesterday.

bjp
01-09-2019, 03:52 PM
WGS kit ordered from Amazon: 17 Jul 2018
FedEx shipping label received from Dante for kit that arrived with no label: 30 Jul 2018
Kit delivered by Fedex: 1 Aug 2018
Email request to receive BAM aligned to hg38: 1 Aug 2018
Email response confirming hg38: 2 Aug 2018
Kit "received" by Dante: 7 Aug 2018
Successful DNA extraction reported: 27 Aug 2018
Sent web request for status update and BAM delivery by hard drive: 9 Dec 2018
Email response confirming HDD will be shipped and sample in sequencing stage: 19 Dec 2018

Nothing since. No blogger rush service for me, but I'm only a very minor one at that (Veritas' first $999 PGP-WGS customer). I wonder if those experiencing delays have also requested hg38 results like I did with this kit (not my DNA this time so I cannot compare it against my Veritas data).

MacUalraig
01-09-2019, 04:03 PM
WGS kit ordered from Amazon: 17 Jul 2018
FedEx shipping label received from Dante for kit that arrived with no label: 30 Jul 2018
Kit delivered by Fedex: 1 Aug 2018
Email request to receive BAM aligned to hg38: 1 Aug 2018
Email response confirming hg38: 2 Aug 2018
Kit "received" by Dante: 7 Aug 2018
Successful DNA extraction reported: 27 Aug 2018
Sent web request for status update and BAM delivery by hard drive: 9 Dec 2018
Email response confirming HDD will be shipped and sample in sequencing stage: 19 Dec 2018

Nothing since. No blogger rush service for me, but I'm only a very minor one at that (Veritas' first $999 PGP-WGS customer). I wonder if those experiencing delays have also requested hg38 results like I did with this kit (not my DNA this time so I cannot compare it against my Veritas data).

I ordered direct the same day you placed yours and had my sample back by 25.7. QA passed 27.8. All I've had since then is one reply with words to the effect that sometimes it has to be run more than once blah blah. I haven't placed an order for the disk results yet.

bjp
01-09-2019, 04:45 PM
I ordered direct the same day you placed yours and had my sample back by 25.7. QA passed 27.8. All I've had since then is one reply with words to the effect that sometimes it has to be run more than once blah blah. I haven't placed an order for the disk results yet.

Sounds like we hit the same QA batch, at least.

"...some of these steps must be repeated several times..." sounds like I got the same blah blah as you did, too.

Ric69
01-10-2019, 10:44 PM
Sounds like we hit the same QA batch, at least.

"...some of these steps must be repeated several times..." sounds like I got the same blah blah as you did, too.

Here was their reply to my inquiry after I had waited half a year: "Thanks For your message. Your sample is undergoing the sequencing process. This is a long and complex process, composed of several steps: sometimes, some of these steps must be repeated several times to obtain the highest possible quality for the genomic data. This can cause delays, but allows us to guarantee the best possible results. Please, let me know if you have any questions. Best regards, Lula"

...and that was TWO MONTHS AGO !!!

Is this starting to sound familiar ???

dufresda
01-11-2019, 02:28 AM
so you waited total 8 months?

Ric69
01-11-2019, 04:27 AM
so you waited total 8 months?

In round numbers, yes approximately. Previous inquiry was late November 2018...

MacUalraig
01-11-2019, 12:03 PM
The CEO posted this a few days ago 'elsewhere'

"Hello, this is Andrea from Dante Labs. I understand you are upset about our delays, and rightly so. Any claim that we are a fraud is false and has no basis whatsoever. We are working hard to make sure people can access advanced genomics at affordable prices, instead of thousands of dollars. We have experienced issues, especially delays, but we have worked with every single user on solving issues, especially delays, providing customized reports free of charge. We won’t abandon anyone."

JamesKane
01-11-2019, 02:38 PM
People are so impatient these days. I remember when it took FTDNA 10 months just to run a single SNP test for DF13 to completion. That's a much less complex procedure than sampling the full 3,099,734,149 bases on the human genome.

Giosta
01-11-2019, 03:18 PM
Kit "received" by Dante: 7 Aug 2018
Successful DNA extraction reported: 27 Aug 2018


20 days ??

bjp
01-11-2019, 03:26 PM
People are so impatient these days. I remember when it took FTDNA 10 months just to run a single SNP test for DF13 to completion. That's a much less complex procedure than sampling the full 3,099,734,149 bases on the human genome.

This is a legitimate point. I laughed at Veritas when they stated they expected completion in 14 weeks for my results as their first WGS customer. I readily expected it to take quite a bit longer (and it did), but I knew I what I was walking into at that point, a brand new pipeline for the company. So I did not let it disappoint me at all or color my impression of them. But that was a limited access pilot with a tiny customer pool, not the competitive marketplace we have now with these companies selling sequencing at discounted rates for promotions.

I'm going to continue being patient, I'm not upset with them yet. And if they provide my BAM on disk and align directly to hg38 I'll end up with results more immediately useful for this sample than I received from Veritas where I realigned them to hg38 myself and downloaded a huge BAM.

bjp
01-11-2019, 03:26 PM
20 days ??

27 days, if you go by when the shipper reports it was delivered to Dante, but yeah. not long at all for the DNA extraction/QC step. Sequencing is another matter.

poi
01-11-2019, 05:26 PM
This is a legitimate point. I laughed at Veritas when they stated they expected completion in 14 weeks for my results as their first WGS customer. I readily expected it to take quite a bit longer (and it did), but I knew I what I was walking into at that point, a brand new pipeline for the company. So I did not let it disappoint me at all or color my impression of them. But that was a limited access pilot with a tiny customer pool, not the competitive marketplace we have now with these companies selling sequencing at discounted rates for promotions.

I'm going to continue being patient, I'm not upset with them yet. And if they provide my BAM on disk and align directly to hg38 I'll end up with results more immediately useful for this sample than I received from Veritas where I realigned them to hg38 myself and downloaded a huge BAM.

It is great that the customers are being impatient, pushing for updates, thus implicitly asking for faster processing, simply because that will only speed up the industry to come up with more efficient pipelines, so will end up with competition for faster processing, which means less waiting, which will definitely mean higher demand, and more companies falling suit, then lower prices, and eventually turning this whole thing into a commodity. Even already, during promos, it cost less than $200 for 30x WGS(though they could be losing money and/or making up by selling the data). And $200 might become the norm in a year or so, then promos will have them for $100.

Erikl86
01-12-2019, 07:52 AM
I've just sent mine back with UPS yesterday. Now the long wait for the results.

Ric69
01-14-2019, 06:53 PM
I would be VERY interested to know if ANYONE has obtained results since July 1, 2018 ??? Based on the above conversations it appears doubtful, or if so the samples were submitted considerably prior to July of last year. By all appearances the pipeline is not just running slow, it seems to be frozen. I would like to believe that is not correct, but my faith in Dante Labs is struggling. Would like to know WHEN you submitted a sample, and WHEN you got results (or if you're still waiting, like me). My intuition tells me there is something dreadfully wrong with this process, and Dante is not being completely candid with us about the delay issues. I'd love to hear from you.

MacUalraig
01-14-2019, 07:03 PM
Well for comparison when I did my Y Elite 1.0 back in 2013 it took about 5 months. My wait at Dante so far is similar so its not out of this world.

dufresda
01-15-2019, 12:29 AM
:\:\:\:\:\:\

dufresda
01-15-2019, 12:46 AM
I would be VERY interested to know if ANYONE has obtained results since July 1, 2018 ??? Based on the above conversations it appears doubtful, or if so the samples were submitted considerably prior to July of last year. By all appearances the pipeline is not just running slow, it seems to be frozen. I would like to believe that is not correct, but my faith in Dante Labs is struggling. Would like to know WHEN you submitted a sample, and WHEN you got results (or if you're still waiting, like me). My intuition tells me there is something dreadfully wrong with this process, and Dante is not being completely candid with us about the delay issues. I'd love to hear from you.

I second this...I wonder if there a more serious matter, a freeze rather than a delay. Anyway can't do anything but wait just wish there was more transparency.

MacUalraig
01-15-2019, 02:01 PM
Well for comparison when I did my Y Elite 1.0 back in 2013 it took about 5 months. My wait at Dante so far is similar so its not out of this world.

I also just checked my 2015 WGSx4 test:
ordered 20.5.15
got kit 27.5.15
back at fgc 6.6.15
results 28.11.15

Helves
01-16-2019, 05:48 PM
So how do you get a hold of your raw data from Dante Labs once they've completed the process?

pinoqio
01-16-2019, 08:18 PM
I sent them some questions about WholeGenomeZ before ordering:

> If there is an option to download the raw data files without an additional charge

A direct download of BAM and FASTQ files will definitely be available in the future,
but I cannot give you an ETA. The HDD option is the fastest way to receive the raw data.
You can find more information at this link. dantelabs.com/products/500-gb-hard-disk-containing-your-raw-data
I don't think this is accurate, since the individual WGS and WES kits both advertise free download.
So there isn't really a reason why they couldn't do it for the combined kit. But I figure, I'll save that discussion for next year...


> What sequencing technology they'd use (ordering from western europe)

We will use the latest BGI platform, the MGI-2000.

> If the backlog has gotten any better

It is true that some of our customer have experienced delays, but we have recently up-scaled our laboratory to deal with the increased workload.

So I guess the only real news is that they are (planning on?) using the MGISEQ-2000,
which on first glance seems to be a scaled up version of the previous BGISEQ-500. (MGI is a subsidary of BGI)

Getting the datasheets from the BGI website is kind of a pain, so here are some direct links:
MGISEQ-2000: en.mgitech.cn/include/upload/kind/file/20181013/20181013145024_8175.pdf
Sequencing Platform Overview: en.mgitech.cn/include/upload/kind/file/20181013/20181013145024_8175.pdf
Adapter Sequences: en.mgitech.cn/include/upload/kind/file/20181108/20181108161128_5692.pdf

Giosta
01-17-2019, 09:24 AM
How big the files are from Dante WGS ? Are the files one single file or multiple files ?

- vcf ... how big, single or multiple
- fastq ... how big, single or multiple
- bam ... how big, single or multiple

I would like to see dir or ls -l command output of these files.

Petr
01-17-2019, 07:42 PM
.:
total 5814016
-rw-rw-r-- 1 petr petr 5309446175 Mar 26 2018 15001702300780A.gvcf.gz
-rw-rw-r-- 1 petr petr 3928458 Mar 26 2018 15001702300780A.gvcf.gz.tbi
-rw-rw-r-- 1 petr petr 51987368 Mar 26 2018 15001702300780A.raw.indel.vcf.gz
-rw-rw-r-- 1 petr petr 186253813 Mar 26 2018 15001702300780A.raw.snp.vcf.gz
-rw-rw-r-- 1 petr petr 200953836 Mar 26 2018 15001702300780A.raw.vcf.gz
drwxrwxr-x 2 petr petr 4096 Jan 4 04:35 clean_data
drwxrwxr-x 2 petr petr 4096 Jan 7 00:38 result_alignment
drwxrwxr-x 6 petr petr 4096 Jun 21 2018 result_variation

./clean_data:
total 214511988
-rw-rw-r-- 1 petr petr 275 Mar 23 2018 15001702300780A.xls
-rw-rw-r-- 1 petr petr 52316575938 Jan 4 04:29 15001702300780A_1.fq.gz
-rw-rw-r-- 1 petr petr 57513362931 Jan 4 04:54 15001702300780A_2.fq.gz
-rw-rw-r-- 1 petr petr 22478 Mar 23 2018 CL100060446_L01_525.base.png
-rw-rw-r-- 1 petr petr 7602 Mar 23 2018 CL100060446_L01_525.qual.png
-rw-rw-r-- 1 petr petr 6870043832 Mar 23 2018 CL100060446_L01_525_1.fq.gz
-rw-rw-r-- 1 petr petr 7608703768 Mar 23 2018 CL100060446_L01_525_2.fq.gz
-rw-rw-r-- 1 petr petr 21871 Mar 23 2018 CL100060446_L01_526.base.png
-rw-rw-r-- 1 petr petr 14491 Mar 23 2018 CL100060446_L01_526.qual.png
-rw-rw-r-- 1 petr petr 7230636852 Mar 23 2018 CL100060446_L01_526_1.fq.gz
-rw-rw-r-- 1 petr petr 8102746436 Mar 23 2018 CL100060446_L01_526_2.fq.gz
-rw-rw-r-- 1 petr petr 21736 Mar 23 2018 CL100060446_L01_527.base.png
-rw-rw-r-- 1 petr petr 7680 Mar 23 2018 CL100060446_L01_527.qual.png
-rw-rw-r-- 1 petr petr 5821152683 Mar 23 2018 CL100060446_L01_527_1.fq.gz
-rw-rw-r-- 1 petr petr 6425974886 Mar 23 2018 CL100060446_L01_527_2.fq.gz
-rw-rw-r-- 1 petr petr 22012 Mar 23 2018 CL100060446_L01_528.base.png
-rw-rw-r-- 1 petr petr 7677 Mar 23 2018 CL100060446_L01_528.qual.png
-rw-rw-r-- 1 petr petr 3988414476 Mar 23 2018 CL100060446_L01_528_1.fq.gz
-rw-rw-r-- 1 petr petr 4416272033 Mar 23 2018 CL100060446_L01_528_2.fq.gz
-rw-rw-r-- 1 petr petr 21464 Mar 23 2018 CL100060446_L01_529.base.png
-rw-rw-r-- 1 petr petr 7635 Mar 23 2018 CL100060446_L01_529.qual.png
-rw-rw-r-- 1 petr petr 6585857335 Mar 23 2018 CL100060446_L01_529_1.fq.gz
-rw-rw-r-- 1 petr petr 7262479360 Mar 23 2018 CL100060446_L01_529_2.fq.gz
-rw-rw-r-- 1 petr petr 21777 Mar 23 2018 CL100060446_L01_530.base.png
-rw-rw-r-- 1 petr petr 7628 Mar 23 2018 CL100060446_L01_530.qual.png
-rw-rw-r-- 1 petr petr 6443802010 Mar 23 2018 CL100060446_L01_530_1.fq.gz
-rw-rw-r-- 1 petr petr 6994896005 Mar 23 2018 CL100060446_L01_530_2.fq.gz
-rw-rw-r-- 1 petr petr 21574 Mar 23 2018 CL100060446_L01_531.base.png
-rw-rw-r-- 1 petr petr 7665 Mar 23 2018 CL100060446_L01_531.qual.png
-rw-rw-r-- 1 petr petr 7669986762 Mar 23 2018 CL100060446_L01_531_1.fq.gz
-rw-rw-r-- 1 petr petr 8419988346 Mar 23 2018 CL100060446_L01_531_2.fq.gz
-rw-rw-r-- 1 petr petr 21993 Mar 23 2018 CL100060446_L01_532.base.png
-rw-rw-r-- 1 petr petr 7556 Mar 23 2018 CL100060446_L01_532.qual.png
-rw-rw-r-- 1 petr petr 7706681988 Mar 23 2018 CL100060446_L01_532_1.fq.gz
-rw-rw-r-- 1 petr petr 8282302097 Mar 23 2018 CL100060446_L01_532_2.fq.gz

./result_alignment:
total 271704184
-rw-rw-r-- 1 petr petr 17670 Mar 23 2018 15001702300780A.Cumulative.png
-rw-rw-r-- 1 petr petr 14375 Mar 23 2018 15001702300780A.Depth.png
-rw-rw-r-- 1 petr petr 17667 Mar 23 2018 15001702300780A.Insert.png
-rw-rw-r-- 1 petr petr 314 Mar 23 2018 15001702300780A.SummaryTable.xls
-rw-rw-r-- 1 petr petr 109035934793 Mar 23 2018 15001702300780A.bam
-rw-rw-r-- 1 petr petr 8842800 Mar 23 2018 15001702300780A.bam.bai

./result_variation:
total 16
drwxrwxr-x 2 petr petr 4096 Jun 21 2018 cnv
drwxrwxr-x 2 petr petr 4096 Jun 21 2018 indel
drwxrwxr-x 2 petr petr 4096 Jun 21 2018 snp
drwxrwxr-x 2 petr petr 4096 Jun 21 2018 sv

./result_variation/cnv:
total 1928
-rw-rw-r-- 1 petr petr 209 Mar 23 2018 15001702300780A.cnv.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 1667122 Mar 23 2018 15001702300780A.cnv.annot.csv
-rw-rw-r-- 1 petr petr 53432 Mar 23 2018 15001702300780A.cnv.gene.csv
-rw-rw-r-- 1 petr petr 237979 Mar 23 2018 15001702300780A.cnv.xls

./result_variation/indel:
total 88900
-rw-rw-r-- 1 petr petr 130 Mar 23 2018 15001702300780A.coding.indel.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 267 Mar 23 2018 15001702300780A.indel.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 37144186 Mar 23 2018 15001702300780A.indel.annot.csv.gz
-rw-rw-r-- 1 petr petr 20866 Mar 23 2018 15001702300780A.indel.cds.len.png
-rw-rw-r-- 1 petr petr 92690 Mar 23 2018 15001702300780A.indel.cds_annot.csv.gz
-rw-rw-r-- 1 petr petr 3326248 Mar 23 2018 15001702300780A.indel.gene.csv.gz
-rw-rw-r-- 1 petr petr 22093 Mar 23 2018 15001702300780A.indel.len.png
-rw-rw-r-- 1 petr petr 50402149 Mar 23 2018 15001702300780A.indel.vcf.gz

./result_variation/snp:
total 299712
-rw-rw-r-- 1 petr petr 115 Mar 23 2018 15001702300780A.coding.snp.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 278 Mar 23 2018 15001702300780A.snp.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 124935799 Mar 23 2018 15001702300780A.snp.annot.csv.gz
-rw-rw-r-- 1 petr petr 2764393 Mar 23 2018 15001702300780A.snp.cds_annot.csv.gz
-rw-rw-r-- 1 petr petr 3517351 Mar 23 2018 15001702300780A.snp.gene.csv.gz
-rw-rw-r-- 1 petr petr 175675610 Mar 23 2018 15001702300780A.snp.vcf.gz

./result_variation/sv:
total 5560
-rw-rw-r-- 1 petr petr 212 Mar 23 2018 15001702300780A.sv.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 3395010 Mar 23 2018 15001702300780A.sv.annot.csv
-rw-rw-r-- 1 petr petr 148933 Mar 23 2018 15001702300780A.sv.gene.csv
-rw-rw-r-- 1 petr petr 2140017 Mar 23 2018 15001702300780A.sv.xls

Petr
01-17-2019, 07:50 PM
And the 2nd kit:
Download: (+unpacked)

.:
total 397644
drwxrwxr-x 4 petr petr 4096 Jan 17 20:47 15001702300576A.snp.annotation
-rw-rw-r-- 1 petr petr 395108115 Jan 28 2018 15001702300576A.snp.annotation.tar.zip
-rw-rw-r-- 1 petr petr 656218 Jan 28 2018 Genome-Overview-219651-15001702300576A_snp_cds_annot_csv-24Jan2018.zip
-rw-rw-r-- 1 petr petr 11413290 Jan 28 2018 Wellness-and-Longevity-219595-15001702300576A_snp_cds_annot_csv-18Jan26.pdf

./15001702300576A.snp.annotation:
total 8
drwxrwxr-x 3 petr petr 4096 Jan 17 20:47 15001702300576A.indel.annotation
drwxrwxr-x 3 petr petr 4096 Jan 17 20:47 15001702300576A.snp.annotation

./15001702300576A.snp.annotation/15001702300576A.indel.annotation:
total 4
drwxrwxr-x 2 petr petr 4096 Jan 17 20:47 annotationResult

./15001702300576A.snp.annotation/15001702300576A.indel.annotation/annotationResult:
total 84696
-rw-rw-r-- 1 petr petr 130 Jan 14 2018 15001702300576A.coding.indel.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 267 Jan 14 2018 15001702300576A.indel.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 35865809 Jan 14 2018 15001702300576A.indel.annot.csv.gz
-rw-rw-r-- 1 petr petr 23859 Jan 14 2018 15001702300576A.indel.cds.len.png
-rw-rw-r-- 1 petr petr 94254 Jan 14 2018 15001702300576A.indel.cds_annot.csv.gz
-rw-rw-r-- 1 petr petr 3314077 Jan 14 2018 15001702300576A.indel.gene.csv.gz
-rw-rw-r-- 1 petr petr 24893 Jan 14 2018 15001702300576A.indel.len.png
-rw-rw-r-- 1 petr petr 47380272 Jan 14 2018 15001702300576A.indel.vcf.gz

./15001702300576A.snp.annotation/15001702300576A.snp.annotation:
total 4
drwxrwxr-x 2 petr petr 4096 Jan 17 20:47 annotationResult

./15001702300576A.snp.annotation/15001702300576A.snp.annotation/annotationResult:
total 1246880
-rw-rw-r-- 1 petr petr 115 Jan 14 2018 15001702300576A.coding.snp.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 278 Jan 14 2018 15001702300576A.snp.AnnotationTable.xls
-rw-rw-r-- 1 petr petr 125224683 Jan 14 2018 15001702300576A.snp.annot.csv.gz
-rw-rw-r-- 1 petr petr 2771565 Jan 14 2018 15001702300576A.snp.cds_annot.csv.gz
-rw-rw-r-- 1 petr petr 3530311 Jan 14 2018 15001702300576A.snp.gene.csv.gz
-rw-rw-r-- 1 petr petr 967837343 Jan 14 2018 15001702300576A.snp.vcf
-rw-rw-r-- 1 petr petr 177419576 Jan 14 2018 15001702300576A.snp.vcf.gz


HDD:

./clean_data_new:
total 97145820
-rw-rw-r-- 1 petr petr 48420521790 Jun 26 2018 15001702300576A_1.fq.gz
-rw-rw-r-- 1 petr petr 51056777115 Jun 26 2018 15001702300576A_2.fq.gz

./result_alignment:
total 310075308
-rw-rw-r-- 1 petr petr 8859496 Mar 8 2018 15001702300576A.bai
-rw-rw-r-- 1 petr petr 87171450210 Mar 8 2018 15001702300576A.bam

Giosta
01-18-2019, 09:36 PM
Thanks. Now i know the gvcf will be about 5.3 Gigabytes

> -rw-rw-r-- 1 petr petr 5309446175 Mar 26 2018 15001702300780A.gvcf.gz
> -rw-rw-r-- 1 petr petr 3928458 Mar 26 2018 15001702300780A.gvcf.gz.tbi

And your two bam files are huge. 109 and 87 Gigabytes

> -rw-rw-r-- 1 petr petr 109035934793 Mar 23 2018 15001702300780A.bam
> -rw-rw-r-- 1 petr petr 8842800 Mar 23 2018 15001702300780A.bam.bai

> -rw-rw-r-- 1 petr petr 87171450210 Mar 8 2018 15001702300576A.bam
> -rw-rw-r-- 1 petr petr 8859496 Mar 8 2018 15001702300576A.bai

And there will be multiple huge fastq files, i don't know what to do with those. Maybe something in the future.

JamesKane
01-19-2019, 07:43 PM
End users don't need the FASTQ files, if you have the BAM for a WGS test. Your BAM contains all the raw FASTQ data with the meta-data that associates the reads to a location on the human reference genome when they can be assessed. These files can always be reverted to FASTQ later.

Ric69
01-23-2019, 04:19 AM
I would be VERY interested to know if ANYONE has obtained results since July 1, 2018 ??? Based on the above conversations it appears doubtful, or if so the samples were submitted considerably prior to July of last year. By all appearances the pipeline is not just running slow, it seems to be frozen. I would like to believe that is not correct, but my faith in Dante Labs is struggling. Would like to know WHEN you submitted a sample, and WHEN you got results (or if you're still waiting, like me). My intuition tells me there is something dreadfully wrong with this process, and Dante is not being completely candid with us about the delay issues. I'd love to hear from you.
I would sort of expect some healthy discussion about data results, science, interpretations of data from Dante Labs if the data were at least trickling in. I see no evidence of that in the past half year. Not just the unbearably long wait times, but seemingly NOTHING in the pipeline trickling in from this lab. Nothing. I'm starting to worry. I have been waiting since June 2018. I would suppose that if someone had sent in samples, say, on May 2018, and it took 6 months, there would be some people here talking about it circa November 2018. ...Crickets. I would love to hear if anybody is getting results from this lab AT ALL ??? And if so, when? Anything recent?

Giosta
01-23-2019, 11:09 AM
One person wrote in Facebook he received Dante gvcf 26 sep 2018

Second person wrote he received gvcf 28 aug 2018 and bam (hard disk) 7 nov 2018

MacUalraig
01-24-2019, 04:38 PM
Did Dante pull their WES test? I don't see it listed anymore. The last Wayback machine copy of their site from Aug 27th 2018 had it listed.

https://web.archive.org/web/20180827020544/https://www.dantelabs.com/

pinoqio
01-24-2019, 05:08 PM
Their pricing seems very volatile, WES was available just two days ago. On the other hand, WGS seems to be back down to 300€ if you don't need the general health report and use the coupon DAZZLE4RARE. They probably removed WES so they can still sell GenomeZ at the normal price, and you can't get it cheaper by ordering WES+WGS separately.

MacUalraig
01-24-2019, 05:37 PM
I'd fancied getting a WES test too but as I have their WGS on order the current combos don't suit me. You can get a WES from FGC for USD525 - its tucked away under 'Analysis and More' in their product drop down list.

MacUalraig
01-24-2019, 05:41 PM
I sent them some questions about WholeGenomeZ before ordering:

> If there is an option to download the raw data files without an additional charge

I don't think this is accurate, since the individual WGS and WES kits both advertise free download.


If you look carefully though, the product page starts off claiming

"VCF, BAM and FASTQ files available for download"

but further down the page it admits...

"Reach out to us for more details if you want to get FASTQ and BAM as well"

which I expect leads you to their new-ish order form for the HD option.

A generous interpretation is that they've forgotten to keep all their statements in synch.

pinoqio
01-24-2019, 08:02 PM
Looking at my browser history, I found the direct link to WES, and it seems you can still order it: dantelabs.com/products/whole-exome-sequencing
And on that page, the claim about BAM&FASTQ being free of charge is unequivocal ;)
Of course, for WES it is quite a bit smaller. I'll just hope they will have a download option by the time they are done sequencing my sample.

dufresda
01-25-2019, 12:22 AM
My thing with Dante Labs is they promised at the end of month three times, did they just say that to me? or is something dependent in process broken that is delaying results and they expected a fix or upgrade and it has not been done as anticipated.

They mention few times I am at final stage sequencing was done just bioinformatics analysis it seems. because repeated steps simply does not satisfy everybody's DNA sample does not make sense machine would have to be broke to repeatedly redo samples for over four months.

If that's the case why can't that be transparent , I don't want to believe it was all a lie to get DNA, but if something in process is taking longer to fix why not communicate that. Clearly something is wrong beyond normal process of just standard repeating.

JamesKane
01-25-2019, 01:12 AM
The analysis of WGS tests is processing heavy. It takes nearly 12 hours on the pipeline I use with an 8 physical core machine. That is just calling the Y chromosome. It’s a few more hours more to call the rest. Add in the other reports and you can see why getting things out the door can take time.

Granted a for profit should be working to cut their timelines down...

J Man
01-25-2019, 06:44 PM
Got another update today.

Dante Labs: Successful DNA extraction - Level A

poi
01-25-2019, 08:33 PM
Got another update today.

Dante Labs: Successful DNA extraction - Level A

Nice. I checked mine and it also says "Status - Success DNA - A"

Ric69
01-26-2019, 12:05 AM
One person wrote in Facebook he received Dante gvcf 26 sep 2018

Second person wrote he received gvcf 28 aug 2018 and bam (hard disk) 7 nov 2018

FWIW, Marco Pezzano reported on FB that he bought the kit on July '18, got results January '19. Looks like some results are trickling out.

dufresda
01-26-2019, 01:30 AM
Why no exact date ? Does not seem believable seem like they made there money and ran

MacUalraig
01-26-2019, 06:35 PM
Why no exact date ? Does not seem believable seem like they made there money and ran

Alert the authorities:

https://www.sec.gov/cgi-bin/browse-edgar?action=getcompany&CIK=0001729314&owner=exclude&count=40

https://www.sec.gov/Archives/edgar/data/1729314/000172931418000002/dantefilingpackage.pdf

https://www.seedinvest.com/dante.labs/seed

But seriously, ran where? And with what? Nx$199 they made from their Black Friday sale?

dufresda
01-27-2019, 05:45 AM
Lol just trolling .....im hopping for the best which should not be the case seems things have gone silent . I asked for a refund and nothing. I got it when it was 350 not 199 so I have been waiting a very long time. What can I do? I complained recieved promises that were not delivered I asked for refund no response. So I guess the money is just gone. It just leaves a very sour taste becuase this is where my DNA is, its my doing but its like now even my Genome is just out there and even with a refund nothing to show for the time just very discouraging sorry for being bitter but its quite angering.

All forgiven now that thats out good day

JamesKane
01-27-2019, 12:42 PM
It's important to keep in mind you with any service, there are three opposing factors. You can choose two of cheap, fast and quality. Right now if you want fast and quality, you will also need to invest over $1,200 for a 30x WGS test. Dante is exploring the cheap and quality axis to get broader adoption. There can be up to a year involved before you see the sample delivered to the partner, sequenced, and finally run through an alignment and calling platform. This is exactly the level of service early adopters saw for Big Y even though FTDNA keeps everything in house.

The third pair (cheap and fast) is really only covered by the Illumina chip sequencing tools. The trade off is only get a report of 600,000 locations versus the 3 billion in your genome.

Erikl86
01-28-2019, 04:13 PM
And update... finally got an email from them that my kit was received today. Now the long journey of awaiting results has began...

Giosta
02-01-2019, 12:35 PM
Dante WGS seems to be 259 eur for now, but when i tried that old discount code, the price dropped to 159 eur ... :)

pinoqio
02-01-2019, 01:47 PM
Looks like the 259€ price is only available to patients diagnosed with a rare disease:

To qualify, patients simply need to upload their diagnosis after their order is placed. The promotion will run from February 1st -28th (Rare Disease Day) and is reserved to rare disease patients. Standard users will still benefit from a special discounted price ($399/€349).dantelabs.com/blogs/news/dante-labs-launches-rare-disease-month-february-2019-with-special-genetic-testing-offering-reserved-for-rare-disease-patients

Giosta
02-01-2019, 04:03 PM
Looks like the 259€ price is only available to patients diagnosed with a rare disease

Ok.

However I have Dante's offer in my mailbox. And no word about sending diagnosis or so ..

***
Dante Labs Offers €259 Whole Genome Sequencing on "Rare Disease Month"

Hello Xxxxx,

Dante Labs is excited to launch today the exclusive Whole Genome Sequencing Service for the month of February 2019 - Rare Disease Month 2019, at the special price of €259.

Get WGS at €259

Dante Labs' purpose is to spread awareness by demonstrating how Next-Generation Sequencing (NGS) can create a significant impact by helping undiagnosed/misdiagnosed patients find long sought-after answers.

The revenues will fund free genetic tests for people in need.
***

pinoqio
02-01-2019, 04:22 PM
Aaand it's gone, DAZZLE4RARE is no longer valid. Did you get an order in before they nixed it?

Giosta
02-01-2019, 04:24 PM
No i didn't. I just tested the code ...

Donwulff
02-03-2019, 09:40 AM
Ugh, I hate when companies with clearly good intention botch the marketing. I already got my DNA done by Dante Labs couple of years back, so I didn't really look into this offer in detail, but I too received the e-mail saying it's €259 for all and a curious mention the profits are used for free tests.

However, on the order page it states "If you seek to get a Customized Report on a disease or gene panel, after receiving your saliva collection kit, fill out the form." where you provide the diagnostics, so it would *seem* like providing diagnostics and medical data to them is still optional. The €349.00 standard service may still be better deal, because it includes " reports on 200+ common diseases, 50+ wellness and longevity traits, reaction to 150+ drugs", while the lower price includes only customized report/panel on the suspected condition. Both include raw data which could be ran through reporting on Sequencing.com, Promethease.com or provided to doctors of course.

They should really make it clearer if the lower price is available to everybody or if they're actually going to demand diagnosis, and yeah that e-mail making no mention of it (even though they link to the press release saying so) is confusing.

Ric69
02-05-2019, 12:06 AM
New review for Dante Labs on medgadget.com
It's not independent in that the reviewer got it for free and thus Dante Labs knew there was going to be a review, but it does look like a genuine outside review.
I, on the other hand, sent the sample in 11 weeks ago now, with Dante Labs stating I'd receive results within couple of weeks three weeks ago, so I'm inclined to think it's a scam. As said, it wouldn't be the first time a DNA company misses delivery estimates, but given the campaign prices are so far below going price/materials price (Human whole genome sequencing at BGI starts at $600, Illumina is couple hundred more) with no plan to cover the price difference presented that they have burden of proof.
There is also a first "Verified Purchase" review on Amazon, but it sounds & looks like Dante Labs press release. My reading is that they ordered the test on 5th September so could not actually have received the results in any case (Which is quite confusing, why admit it was ordered three weeks ago if the processing time is eight weeks?)
Sequencing.com, their biinformatics analytics partner, has been listing Dante Labs as their "preferred provider" for a while though.

That is a VERY old review, 2017 (as was your comment, also 2017)

Ric69
02-07-2019, 05:34 AM
Update: Received my VCF file today. (exactly 233 days since I mailed in the sample). I'll update again when I get the reports and (more importantly) the BAM file.

Donwulff
02-07-2019, 07:05 PM
I sent them some questions about WholeGenomeZ before ordering:
So I guess the only real news is that they are (planning on?) using the MGISEQ-2000,
which on first glance seems to be a scaled up version of the previous BGISEQ-500. (MGI is a subsidary of BGI)


Based on the datasheet that's actually capable of 150basepair paired-end sequencing. If they'll be using that flowcell, that'll remove the main disadvantage compared to Illumina sequencing which are often 150-160bp. Of course, don't see statistics on quality yet, there's more read-errors the further the read proceeds, the quality could go down more on their platform. But that's interesting, the issue of capacity could always be solved by having more sequencers. I'm sure at the prices Dante Labs is offering, they must be using spare capacity when the lab has nothing better paying to sequence, so improved capacity definitely helps there.

reignman
02-08-2019, 12:31 PM
Update: Received my VCF file today. (exactly 233 days since I mailed in the sample). I'll update again when I get the reports and (more importantly) the BAM file.

E-mail them and request BAM and FASTQ files on hard drive and links.
I have been waiting almost 3 months for BAM and FASTQ files.
Do you plan do analyze your VCF file?

Ric69
02-08-2019, 06:51 PM
E-mail them and request BAM and FASTQ files on hard drive and links.
I have been waiting almost 3 months for BAM and FASTQ files.
Do you plan do analyze your VCF file?

Have done a preliminary look-see using Promethease and Sequencing.com viewers. Those are limited but do have useful links to medline and the NIH database and other annotation libraries. I'm more interested in the BAM/FASTQ file to do more serious analysis (using Galaxy and other toolsets). Yes, have formally requested those files. Wish it were more expiditious, say using dropbox, google cloud, or even Big Yotta (sequencing.com's favorite). Putting it on a hard drive seems inefficient and not cost-effective (and slow).

dufresda
02-10-2019, 10:05 PM
Finally got the VCF raw data available today which is not as useful as my awaiting BAM files on HDD

ianz91
02-11-2019, 04:43 AM
So I looked up this Dante Labs and can't find if they do autosomal testing, am I missing something? Do they have any ancestry tests?

Jatt1
02-11-2019, 05:19 AM
So I looked up this Dante Labs and can't find if they do autosomal testing, am I missing something? Do they have any ancestry tests?

Yes, it is WGS[whole genome sequencing. You get all your aDNA, yDNA and mtDNA in one shot. 23andme etc do only a tiny part of what WGS does.

ianz91
02-11-2019, 05:52 AM
Yes, it is WGS[whole genome sequencing. You get all your aDNA, yDNA and mtDNA in one shot. 23andme etc do only a tiny part of what WGS does.

Do they actually show what your ancestry is, or do I have to download the data and upload it somewhere else?

Jatt1
02-11-2019, 11:55 AM
Do they actually show what your ancestry is, or do I have to download the data and upload it somewhere else?

Don't know much about that. YFull will get you yDNA and mtDNA and you be on YFUllTree. For aDNA you may have to use a tool or get someone else to extract info for SNPs that are on other tests, Generalissimo and many more here should be able to guide in that. And then you can use all WGS data to get medical reports on you from many sources also.

JamesKane
02-11-2019, 12:24 PM
Do they actually show what your ancestry is, or do I have to download the data and upload it somewhere else?

You will need to upload the data somewhere else. This test should be considered cutting-edge for autosomal applications. You need to use something like the emerging genomic application marketplaces like sequencing.com to make sense of the data if you're not a bioinformatician.

aaronbee2010
02-11-2019, 12:27 PM
Do they actually show what your ancestry is, or do I have to download the data and upload it somewhere else?

I believe you're able to upload the .VCF file you get from your WGS results to GEDmatch, however there are a couple of extra steps. It's all pretty easy though, and there are plenty of people on Anthrogenica who can help. So ancestry is covered there.

Dante Labs (or any other WGS vendor for that matter) don't provide an ancestry report themselves as far as I know (if that's what you're asking).

reignman
02-11-2019, 02:18 PM
I believe you're able to upload the .VCF file you get from your WGS results to GEDmatch, however there are a couple of extra steps. It's all pretty easy though, and there are plenty of people on Anthrogenica who can help. So ancestry is covered there.

Dante Labs (or any other WGS vendor for that matter) don't provide an ancestry report themselves as far as I know (if that's what you're asking).

Recent VCF files from Dante Labs are HG38, while GedmatchGenesis accepts only HG19. Maybe someone can write on this thread a short step by step guide how to lift-over VCF file. Many people do not know how to do it.

Helves
02-11-2019, 04:41 PM
Recent VCF files from Dante Labs are HG38, while GedmatchGenesis accepts only HG19. Maybe someone can write on this thread a short step by step guide how to lift-over VCF file. Many people do not know how to do it.

Which one of Dante Labs tests would you recommend someone mainly interested in getting as good raw data as possible from them to upload it to third party websites(such as Gedmatch). I'm not interested in finding more about my haplogroups.

JamesKane
02-11-2019, 04:51 PM
You really only need the 30x WGS test for genealogical information. The WES and Whole GenomeZ products are mostly to get very accurate results on the gene encoding regions. WES is not terribly useful for us as genealogical applications of DNA mostly deal with the "junk" regions.

Tonev
02-11-2019, 06:29 PM
Recent VCF files from Dante Labs are HG38, while GedmatchGenesis accepts only HG19. Maybe someone can write on this thread a short step by step guide how to lift-over VCF file. Many people do not know how to do it.

I have uploaded my Dantelabs HG38 VCF fle on Gnesis. They had accepted it with no comments...

ianz91
02-12-2019, 12:30 AM
Yeah I think I'll pass on this one, it's expensive and I don't want to run around to different places just to see my ancestry.

ssamlal
02-12-2019, 02:48 AM
Lol just trolling .....im hopping for the best which should not be the case seems things have gone silent . I asked for a refund and nothing. I got it when it was 350 not 199 so I have been waiting a very long time. What can I do? I complained recieved promises that were not delivered I asked for refund no response. So I guess the money is just gone. It just leaves a very sour taste becuase this is where my DNA is, its my doing but its like now even my Genome is just out there and even with a refund nothing to show for the time just very discouraging sorry for being bitter but its quite angering.

All forgiven now that thats out good day

I feel your pain bruh. I ordered back in November (2018). Received and mailed the kit in December. About 3 weeks ago they emailed that my sample was unusable and that they would send a new kit. I sent a few emails last week asking for the tracking information but have yet to receive a response (or the new kit). Not impressed!. Will probably check with my credit card company if I can dispute the charge. Too bad I didn't use AMEX (they're good with disputed charges).

Giosta
02-12-2019, 05:45 PM
I ordered Dante wgs sep 2018. Lab received it 3 oct 2019. Today 12 feb 2019 i was able to download the vcf file. This period was 132 days or abt 19 weeks. Vcf file is 144 Megabyte gz (zipped) and abt 950 Megabytes unzipped. It is hg37 despite i ordered hg38 bam and thought vcf would also be hg38. The vcf file contains abt 3,47 million lines data. Y-chr lines are abt 3900. There was no mitochondrio lines (chrM) at all.

I spent few hours to search snp names like CTS8565 and then its hg37 position and then tried to search that position number from vcf file. One by one i ended up N-Y19097.

Tonev
02-14-2019, 11:21 AM
I ordered Dante wgs sep 2018. Lab received it 3 oct 2019. Today 12 feb 2019 i was able to download the vcf file. This period was 132 days or abt 19 weeks. Vcf file is 144 Megabyte gz (zipped) and abt 950 Megabytes unzipped. It is hg37 despite i ordered hg38 bam and thought vcf would also be hg38. The vcf file contains abt 3,47 million lines data. Y-chr lines are abt 3900. There was no mitochondrio lines (chrM) at all.

I spent few hours to search snp names like CTS8565 and then its hg37 position and then tried to search that position number from vcf file. One by one i ended up N-Y19097.

Concerning searching SNPs, as I shared my experience at the beginning of January, I did a simple MS Access query with two tables: table 1. my Y-DNA fraction from the VCF (excel) + table 2. the latest ISOGG Y-DNA index file (also excel). I connected them with Common column: Position (Build 37 Number) because my VCF file was Build 37. The MS Access query did the rest of the work- it compared all positions and returned only the intersections (SNPs) in the two tables. That way I found my deepest SNP: G-Z44370, known up to now.
Concerning timeframe- it appears a typical case around here: Kit ordered on 15 August 2018, Dante Lab received the Kit on 30 Sept. 2018, VCF received at the beginning of December ... and waiting since then BAM + FASTQ files (which most ridiculously- turned out that had to be excplicitly ordered despite the fact that they were included in the August price). Since then up to now (2+ months later)- nothing from Dante Labs, no reply to my questions, no tracking information for a posted HDD, no nothing.

MacUalraig
02-14-2019, 11:49 AM
Yes I've got a mySQL db for all my VCF and SNP analysis and do a similar thing.

Tonev
02-14-2019, 12:01 PM
Yes I've got a mySQL db for all my VCF and SNP analysis and do a similar thing.

I am not so familiar with other tools/apps and tried to use what I had :)

Giosta
02-14-2019, 02:20 PM
I asked Dante what to do with my second kit because the tube does not contain kit number, 14 numbers long. This second tube has only a bar code and two short numbers like 1234 5678. Now i don't know how to register my second kit. And no answer from Dante.

I would like to have BAM and FASTQ file download link. I don't want a hard drive. Should i order those download links or what? I guess the links don't cost anything?

MacUalraig
02-14-2019, 03:39 PM
I asked Dante what to do with my second kit because the tube does not contain kit number, 14 numbers long. This second tube has only a bar code and two short numbers like 1234 5678. Now i don't know how to register my second kit. And no answer from Dante.

I would like to have BAM and FASTQ file download link. I don't want a hard drive. Should i order those download links or what? I guess the links don't cost anything?

I'm just a punter like you but my understanding is that if you want the BAM/FASTQ you have to order it on disk. The download link is what we call 'vaporware'.

aaronbee2010
02-15-2019, 03:15 PM
Whole Genome Sequence with mtDNA for 199.00 with discount code: JUSTFORME199

Offer only valid until Sunday 17th February

Afshar
02-15-2019, 08:08 PM
Makes me wonder what is the catch

aaronbee2010
02-15-2019, 08:09 PM
Makes me wonder what is the catch

Waiting about a year for your results :P

Jatt1
02-15-2019, 08:22 PM
Whole Genome Sequence with mtDNA for €199.00 with discount code: JUSTFORME199

Offer only valid until Sunday 17th February

Sunday in China is actually Saturday in Americas.

aaronbee2010
02-15-2019, 08:24 PM
Sunday in China is actually Saturday in Americas.

:O

These AG users really do not have long then!

khanabadoshi
02-15-2019, 08:28 PM
Whole Genome Sequence with mtDNA for €199.00 with discount code: JUSTFORME199

Offer only valid until Sunday 17th February


The discount code didn't work on the US site.

aaronbee2010
02-15-2019, 08:33 PM
The discount code didn't work on the US site.

Can you go on the regular Dante Labs and order from there if you're a US resident? The code works on there.

khanabadoshi
02-15-2019, 08:35 PM
Can you go on the regular Dante Labs and order from there if you're a US resident? The code works on there.

It seems to keep redirecting me to us.dantelabs.com. I went ahead and ordered it without the discount code, because it's still a pretty good deal.

aaronbee2010
02-15-2019, 08:37 PM
It seems to keep redirecting me to us.dantelabs.com. I went ahead and ordered it without the discount code, because it's still a pretty good deal.

I would've used a VPN in that case. You have ordered it anyways though. Good job!

khanabadoshi
02-15-2019, 08:39 PM
I would've used a VPN in that case. You have ordered it anyways though. Good job!

I have a VPN and thought about it only afterwards. LOL... oh well.

aaronbee2010
02-15-2019, 08:43 PM
I have a VPN and thought about it only afterwards. LOL... oh well.

Press F to pay respects

JamesKane
02-16-2019, 01:24 AM
For those who took this test for Y-DNA coverage, this is roughly the coverage you can expect on the more useful part:

https://haplogroup-r.org/data/histograms/Dante-30x%20WGS.png

poi
02-16-2019, 01:47 AM
Any tips on how to convince da wife that this is a really good deal so that I can get a few kits for the family?

I already ordered WGS from DanteLab in November, so while I'm waiting for my data, I want my wife and kids to get tested. The price is right with this current deal, but need to convince her that WGS is worth it and is future proof since it is medical grade 30x. She did not even think my $50 23andme purchase was worth it (and eventually gave in after months of persuasion). So, it can be done. But $250+ is a bit of a hard sell and I don't have much time before the deal expires in 24 hours.

Jatt1
02-16-2019, 06:40 AM
Any tips on how to convince da wife that this is a really good deal so that I can get a few kits for the family?

I already ordered WGS from DanteLab in November, so while I'm waiting for my data, I want my wife and kids to get tested. The price is right with this current deal, but need to convince her that WGS is worth it and is future proof since it is medical grade 30x. She did not even think my $50 23andme purchase was worth it (and eventually gave in after months of persuasion). So, it can be done. But $250+ is a bit of a hard sell and I don't have much time before the deal expires in 24 hours.


Health SNPs, early knowledge leads to early action and better health for all the members of the family, etc.

ianz91
02-16-2019, 11:32 PM
Any tips on how to convince da wife that this is a really good deal so that I can get a few kits for the family?

I already ordered WGS from DanteLab in November, so while I'm waiting for my data, I want my wife and kids to get tested. The price is right with this current deal, but need to convince her that WGS is worth it and is future proof since it is medical grade 30x. She did not even think my $50 23andme purchase was worth it (and eventually gave in after months of persuasion). So, it can be done. But $250+ is a bit of a hard sell and I don't have much time before the deal expires in 24 hours.



"Honey, we should get this test, it will tell you how you are always right, and how you look good in those jeans".

poi
02-17-2019, 06:32 AM
"Honey, we should get this test, it will tell you how you are always right, and how you look good in those jeans".

We compromised. Instead of the whole family, just bought 1 additional kit (used the European site, so paid US $230) this time. When the kit arrives, we will decide whether to test her or one of the kids. Hopefully DanteLab does not void the order, because the US site was showing $299.

Tonev
02-17-2019, 11:22 AM
We compromised. Instead of the whole family, just bought 1 additional kit (used the European site, so paid US $230) this time. When the kit arrives, we will decide whether to test her or one of the kids. Hopefully DanteLab does not void the order, because the US site was showing $299.

So, the promo-code still works as of today? $230 / 199 Euro? Does the price incude the VCF, BAM and FASTQ files, or they will be additionally charged?

aaronbee2010
02-17-2019, 12:39 PM
So, the promo-code still works as of today? $230 / 199 Euro? Does the price incude the VCF, BAM and FASTQ files, or they will be additionally charged?

I just got an email to say today's the last day!

aaronbee2010
02-17-2019, 12:43 PM
So, the promo-code still works as of today? $230 / 199 Euro? Does the price incude the VCF, BAM and FASTQ files, or they will be additionally charged?

And yes, all of those results are included for free.

Giosta
02-17-2019, 08:24 PM
I am not sure if BAM and FASTQ will be free?

aaronbee2010
02-17-2019, 08:43 PM
I am not sure if BAM and FASTQ will be free?

They're included for free.

Giosta
02-17-2019, 10:17 PM
Do you know anyone who has already downloaded their BAM and FASTQ?

My first Dante test is now ready and I am able to download VCF. But not BAM & FASTQ. I can only find a hard disk order about $60 which is not free.

So, is there anyone who has already downloaded his BAM from Dante ??

aaronbee2010
02-17-2019, 10:26 PM
Do you know anyone who has already downloaded their BAM and FASTQ?

My first Dante test is now ready and I am able to download VCF. But not BAM & FASTQ. I can only find a hard disk order about $60 which is not free.

So, is there anyone who has already downloaded his BAM from Dante ??

Ahh this is interesting. Thats not what they say on their website. Can you contact Dante Labs support and see what they say? This isn't good to hear :(

poi
02-19-2019, 05:35 AM
Ahh this is interesting. Thats not what they say on their website. Can you contact Dante Labs support and see what they say? This isn't good to hear :(

$60 for the harddrive was my understanding, as well. VCF would be a download, but they make extra money off the harddrive. Still $60 for a physical drive would be fine, although I would still back the data up in multiple drives and/or cloud locations.

Btw, my most recent order from the non-US site went through (saved $70 or so versus the US site) and I received a tracking number, which shows the kit is being shipped from Utah.

Status
In-Transit
February 18, 2019 at 10:04 pm
Arrived at USPS Regional Origin Facility
SALT LAKE CITY UT NETWORK DISTRIBUTION CENTER

So, they did not void the order. :beerchug:

Giosta
02-19-2019, 10:43 AM
Dante web page still have this text.

"VCF AVAILABLE
VCF, BAM and FASTQ files available for download"

aaronbee2010
02-19-2019, 11:23 AM
$60 for the harddrive was my understanding, as well. VCF would be a download, but they make extra money off the harddrive. Still $60 for a physical drive would be fine, although I would still back the data up in multiple drives and/or cloud locations.

Btw, my most recent order from the non-US site went through (saved $70 or so versus the US site) and I received a tracking number, which shows the kit is being shipped from Utah.

Status
In-Transit
February 18, 2019 at 10:04 pm
Arrived at USPS Regional Origin Facility
SALT LAKE CITY UT NETWORK DISTRIBUTION CENTER

So, they did not void the order. :beerchug:

You should tell this to Khana :P

Tonev
02-19-2019, 11:25 AM
Dante web page still have this text.

"VCF AVAILABLE
VCF, BAM and FASTQ files available for download"

Yes, "available".
The keyword here is "for the same price"? For additional price?

reignman
02-20-2019, 01:26 PM
Yes, "available".
The keyword here is "for the same price"? For additional price?

In an e-mail communication, the agent wrote to me that for discounted WGS price hard disc with BAM and FASTQ files will be additionally charged €59, while links for download will be provided for free.

Few days ago I got answer that Logistic department works on my hard disc with BAM and FASTQ.

bjp
02-20-2019, 03:01 PM
WGS kit ordered from Amazon: 17 Jul 2018
FedEx shipping label received from Dante for kit that arrived with no label: 30 Jul 2018
Kit delivered by Fedex: 1 Aug 2018
Email request to receive BAM aligned to hg38: 1 Aug 2018
Email response confirming hg38: 2 Aug 2018
Kit "received" by Dante: 7 Aug 2018
Successful DNA extraction reported: 27 Aug 2018
Sent web request for status update and BAM delivery by hard drive: 9 Dec 2018
Email response confirming HDD will be shipped and sample in sequencing stage: 19 Dec 2018

Nothing since. No blogger rush service for me, but I'm only a very minor one at that (Veritas' first $999 PGP-WGS customer). I wonder if those experiencing delays have also requested hg38 results like I did with this kit (not my DNA this time so I cannot compare it against my Veritas data).

Initial results for this kit received today, 20 Feb 2019. PDF wellness report, and two VCF download links, one for SNPs, one for indels.

Tonev
02-20-2019, 07:15 PM
In an e-mail communication, the agent wrote to me that for discounted WGS price hard disc with BAM and FASTQ files will be additionally charged €59, while links for download will be provided for free.

Few days ago I got answer that Logistic department works on my hard disc with BAM and FASTQ.

I would like thank to a number of posts here and to dislike even more posts not because of you fellow "customers/...../" of Dante Labs. But because of what Dante had told to each of you in different moment in different context.... Having in mind one and the same- their WGS... Different approaches in identtical situations like in a XVII century countryard market. Once- you have it all online but not really all, once- only vcf, once vcf+indel (for WGS???) , once in 11 weeks, once in 22, once 111 weeks, or maybe never. Some of us- not asking at all and just waiting silently and praying. Some of us- talking, with results ranging from zero, through some price discount to online link, or whatever else... And all of it- for the same WGS of Dante Labs, with endless promotions so that new customer would be guaranteed.... It makes me wonder who is the decision maker there for the small discounts/small gestures - the phone operator? the e-mail operator? the Facebook correpondent? Stopped wondering on what grounds... I hope I have not crossed the good manners, just for the sake of self-respect...

MacUalraig
02-20-2019, 07:26 PM
I would like thank to a number of posts here and to dislike even more posts not because of you fellow "customers/...../" of Dante Labs. But because of what Dante had told to each of you in different moment in different context.... Having in mind one and the same- their WGS... Different approaches in identtical situations like in a XVII century countryard market. Once- you have it all online but not really all, once- only vcf, once vcf+indel (for WGS???) , once in 11 weeks, once in 22, once 111 weeks, or maybe never. Some of us- not asking at all and just waiting silently and praying. Some of us- talking, with results ranging from zero, through some price discount to online link, or whatever else... And all of it- for the same WGS of Dante Labs, with endless promotions so that new customer would be guaranteed.... It makes me wonder who is the decision maker there for the small discounts/small gestures - the phone operator? the e-mail operator? the Facebook correpondent? Stopped wondering on what grounds... I hope I have not crossed the good manners, just for the sake of self-respect...

There does seem to be an element of luck involved in getting a response, but it depends I guess on what you were asking and how often. Personally I don't bombard firms with endless requests for updates, in my experience if its not ready their statements on when it will be ready are scarcely worth reading. By that I'm talking about any firm not just Dante.

I just sent a polite chaser to YSEQ yesterday to enquire about the posting of my BAM disk, I waited a week after getting the online parts. Was that a bit impatient? Anyway I got a reply back today so all is good.

As regards to the format and delivery method of the data, I did an online chat with Chronomics today and got the response 'we are fairly flexible about delivery method'. It's so vague its no better than Dante?

Giosta
02-20-2019, 07:37 PM
Initial results for this kit received today, 20 Feb 2019. PDF wellness report, and two VCF download links, one for SNPs, one for indels.

Two vcf files ?? I have only one available for download (i already downloaded it last week).

Dante has not answered my question about bam download link. Absolutely quiet.

bjp
02-21-2019, 12:56 PM
Two vcf files ?? I have only one available for download (i already downloaded it last week).

Dante has not answered my question about bam download link. Absolutely quiet.

Did your VCF contain indels, or only SNPs? I did not expect two separate files, so I searched a bit and found a six month old post on reddit from someone saying they also received two files, but there was a time delay between the SNP file, which they received first, and the indel file which showed up later: https://www.reddit.com/r/promethease/comments/935kgb/does_promethease_understand_indelvcfgz_files_from/

"I got my indel.vcf.gz file from dante labs today. I recieved the snp-vcf.gz ages ago and had that analyzed by promethease."

First thing I did with these files was run them through vcf-concat and vcf-sort to produce a sorted and merged file, they ran cleanly.

Both files are in VCF 4.2 format and contain variant calls only. Both files are aligned to hg19, not hg38 as I had requested (a minor annoyance for me since I plan to realign all the reads once I have BAM data and produce an hg38 gVCF for all positions, but maybe a problem for customers not familiar with the process).

I will wait a week or so before contacting them to check for an update on the BAM.

Edit to add: the merged/sorted VCF processed just fine through Promethease. Variants reported in almost 17,000 named SNPs. For comparison, the gVCF I generated of my own Veritas data resulted in 99,069 named SNPs but the balance of unlisted SNPs should match the reference sequence.

oagl
02-21-2019, 05:19 PM
If you copy the link for your snp vcf file and replace the snp in the filename with indel then you can download it. At least this worked for me.

Giosta
02-21-2019, 06:00 PM
If you copy the link for your snp vcf file and replace the snp in the filename with indel then you can download it. At least this worked for me.

This works !! Just downloaded 29 Megabyte indel.vcf.gz

I guess similar download link editing would allow me to download the bam file, perhaps ...

Tonev
02-21-2019, 07:37 PM
This works !! Just downloaded 29 Megabyte indel.vcf.gz

I guess similar download link editing would allow me to download the bam file, perhaps ...

I' ve gort my indel too (whatever could be its use). Replaced the name of the file+folder=> it worked...
I remember someone mentioned that he had receive an online link for BAM... what was the name of the file and folder for BAM and FASTQ?

Giosta
02-21-2019, 08:41 PM
I remember someone mentioned that he had receive an online link for BAM... what was the name of the file and folder for BAM and FASTQ?

This is important!
1. is there anyone who have downloaded his BAM from Dante
2. we need the download link (maybe kit number masked) to get path names

I am slightly tired Dante does not answer anything and we have to 'hack' path names to get files we have already paid.

newuser
02-21-2019, 09:22 PM
What is the file size of the vcf of an average wgs?
I ordered the whole genomez ngs.
Got a 3MB for SNP and less than 1MB for in del.
Seems small or not?

How long did you guys had to wait for getting the hard drive sent?

bjp
02-21-2019, 09:37 PM
What is the file size of the vcf of an average wgs?
I ordered the whole genomez ngs.
Got a 3MB for SNP and less than 1MB for in del.
Seems small or not?

How long did you guys had to wait for getting the hard drive sent?

I agree that this seems very small and suspect your downloads may have been interrupted. If you attempt to gunzip the files, does the extraction complete? If not I would try to download again.

For the Dante kit I have just been working with, the snp.vcf.gz was 137MB compressed, 797MB uncompressed. The indel.vcf.gz was 42MB compressed, 215MB uncompressed. For my own results from another vendor, my combined VCF was 384MB compressed, and 2.4GB uncompressed.

No hard drive received yet here.

newuser
02-21-2019, 09:57 PM
Compressed was 3.6MB for snp and uncompressed 18MB.
Redownload is the same size and extracts without issues.
Should I contact support?
Or wait for the hard drive and create the vcf myself.

bjp
02-21-2019, 10:19 PM
I see no risk in contacting support to ask them to confirm that your data processed correctly. I can think of a few possible reasons for such small files, one may be that your files do not contain the same extra details in the VCF INFO column, or are missing quality scores (the kit I am looking at is the plain whole genome product, not the whole genomeZ WES+WGS that you purchased). If you skip past the header lines starting with ## on your file and get to the results, how many columns are populated? In this kit I see for the first called SNP:

chr1 13116 . T G 244.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.472e+00;ClippingRankSum=0.00;DP=17;ExcessHet=3.0 103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.06;MQRankSu m=-3.584e+00;QD=14.40;ReadPosRankSum=-1.468e+00;SOR=0.859;VQSLOD=3.23;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/1:10,7:17:99:0|1:13110_G_A:273,0,565

(OK, the forum turned some of those into emoticons but I think you get the idea)

If none of your data rows contain extra details beyond the 'PASS' column, you may still have complete results without the extra details. The SNP file I have here has about 3.2 million rows, and I can see rows referencing each chromosome. If your file doesn't contain results for each chromosome it may have been truncated on Dante's side before it was made available for you to download.

I would definitely generate my own gVCF file from the BAM data once received.

Thoughts from others?

Ric69
02-22-2019, 02:36 AM
This works !! Just downloaded 29 Megabyte indel.vcf.gz

I guess similar download link editing would allow me to download the bam file, perhaps ...

I tried it, works for indel, snp, not bam.

euasta
02-22-2019, 03:12 PM
Does anyone know if/how to determine haplogroups and ancestors using those files?

MacUalraig
02-23-2019, 11:48 AM
Does anyone know if/how to determine haplogroups and ancestors using those files?

For haplogroup you can either just do it manually which doesn't take that long or you can acquire a list of Y SNPs (off ybrowse for example) and do a database join between the SNP list and the VCF which is fairly straightforward in Excel/Acess/SQL etc. If you are just going to do it once it can be quicker to do it manually. Depends of course how deep your local tree branch is... for example I only need to check about seven levels from R-P312 and I've arrived. That's 7 SNP checks in the VCF.

That's placing you in the known tree. Then when you have the BAM send it to YFull for full analysis including your novel variants.

poi
02-25-2019, 05:44 AM
My Dante lab kit purchased a week ago has arrived. It will likely be sent tomorrow and the waiting game begins. My Nov purchased is still "Status: Success DNA - A", so will see what happens in the next few months with that kit. The latest kit will likely have results around late fall or even in 2020. I hope I'm wrong.

pmokeefe
02-25-2019, 04:48 PM
Today, Feb 25, I received an email from Dante Labs saying my test results were available. I downloaded the SNP vcf file and wellness report from their web site. The compressed vcf file is 148.7MB. I haven't had a chance to look at it yet. I ordered the test on Oct 30, shortly afterwards it was delivered to me in Rome, Italy and I returned it immediately. So a little less than four months. The indel vcf file has not been posted, hopefully that will come shortly. I haven't requested the raw data yet, but I intend to shortly. Anyone had any luck getting their raw data recently (2019?)
As usual, I upload the files to Google Drive, please feel free to use them as you like.
https://drive.google.com/open?id=13T9oMQNj9Ld_fnW2GVvqk7cFWq7-zlsZ
This is the second Dante Labs Test I've taken. Those test results and other are available for comparison in the following Google Drive folder
https://drive.google.com/open?id=1_x7ZtSenJNUyb9nsq0hcNbyizx1a39F3

Tonev
02-25-2019, 07:45 PM
I was recently looking at newly named /unlisted SNPs at ISOGG Wiki, including (https://isogg.org/w/images/c/c4/FTSNPindex.xlsx), (https://isogg.org/w/images/a/ad/BYSNPindex.xlsx) and (https://isogg.org/w/images/5/51/FGCmarkers.20180703.xlsx).
Any ideas whether all of them are incuded in http://ybrowse.org/gbrowse2/gff/snps_hg38.csv?
And what are the usual procedures and timeframe for inclding to the ISOGG Y-DNA index tree?

aaronbee2010
02-25-2019, 09:03 PM
My kit (only 175 at the time) arrived this afternoon. I've collected my saliva in the collection tube, and it's ready to be shipped off tomorrow :)

The results will take a while, but it's definitely worth it for the price!

an38
02-28-2019, 12:43 PM
I' ve gort my indel too (whatever could be its use). Replaced the name of the file+folder=> it worked...
I remember someone mentioned that he had receive an online link for BAM... what was the name of the file and folder for BAM and FASTQ?

Try also ".raw.snp.vcf.gz" and ".raw.indel.vcf.gz".
The interesting part would be the BAM and FASTQ, but no luck for that.

bjp
02-28-2019, 02:01 PM
Try also ".raw.snp.vcf.gz" and ".raw.indel.vcf.gz".
The interesting part would be the BAM and FASTQ, but no luck for that.

Can you describe what if anything differed about the files you downloaded with ".raw" in the name? I've just attempted those with the kit I have access to and did not get anything back (access denied, bad link).

pmokeefe
02-28-2019, 03:48 PM
Can you describe what if anything differed about the files you downloaded with ".raw" in the name? I've just attempted those with the kit I have access to and did not get anything back (access denied, bad link).

I was able to get the ".raw.snp.vcf.gz" yesterday. The ".raw.snp.vcf.gz" was slightly bigger than the ".snp.vcf.gz" file, but I'm not sure what the difference is. I haven't looked at the headers yet. Maybe someone already knows?

an38
02-28-2019, 03:53 PM
Can you describe what if anything differed about the files you downloaded with ".raw" in the name? I've just attempted those with the kit I have access to and did not get anything back (access denied, bad link).

After a quick examination, the raw files have a few more lines (+15%), and they are missing some "##FILTER=" stuff at the beginning.
Basically, there is a bit of stuff that was instead filtered away (because of "Truth sensitivity") from the normal vcf.

MacUalraig
02-28-2019, 04:21 PM
I read a comment somewhere else earlier speculating that they might have shipped out 7k kits? It wasn't clear what the basis for the claim was, possibly he was looking at order sequence numbers or some such. In case so my order number from last July was something like EU18xxW... maybe someone who has ordered more recently could indicate what kind of order number they have? Of course we have no way of knowing whether these actually correspond to sales or not.

poi
02-28-2019, 05:26 PM
I read a comment somewhere else earlier speculating that they might have shipped out 7k kits? It wasn't clear what the basis for the claim was, possibly he was looking at order sequence numbers or some such. In case so my order number from last July was something like EU18xxW... maybe someone who has ordered more recently could indicate what kind of order number they have? Of course we have no way of knowing whether these actually correspond to sales or not.

My kit bought a week ago is: EU52xxW. Note that I bought from their Global site, so the kit might be prefixed "EU". I don't remember what my US-based order was late last year. So, combined US and EU, they might have shipped over 7K kits.

Giosta
02-28-2019, 10:45 PM
Try also ".raw.snp.vcf.gz" and ".raw.indel.vcf.gz".
The interesting part would be the BAM and FASTQ, but no luck for that.

I just downloaded .raw.snp.vcf.gz and .raw.indel.vcf.gz

Thank you very much!

JamesKane
03-01-2019, 12:16 AM
And what are the usual procedures and timeframe for inclding to the ISOGG Y-DNA index tree?

Sometime between now and infinity. The ISOGG tree is volunteer driven and people need to submit the change requests via a process that has no formalization. You'll have better luck waiting on someone like YFULL to include them in their skeleton.

pinoqio
03-01-2019, 12:19 PM
My kit bought a week ago is: EU52xxW. Note that I bought from their Global site, so the kit might be prefixed "EU". I don't remember what my US-based order was late last year. So, combined US and EU, they might have shipped over 7K kits.
Based on my two orders a month apart they had about ~13 orders a day during February (EU site).

MacUalraig
03-02-2019, 09:12 AM
Based on my two orders a month apart they had about ~13 orders a day during February (EU site).

Sounds encouraging, now if they would release 13 results a day too ...

Jan_Noack
03-05-2019, 09:17 AM
Sounds encouraging, now if they would release 13 results a day too ...
Hi, I've just placed an order for another person. He has already done the BigY. A bit early here, but do folk somehow join their BigY and WGS results for the Y part together in a larger BAM. One day I need to understand all of this or find ut someone who does... Just seems an obvious thing to try to do a, so I was wondering if folk have done it or are doing it ? Unsure if you have done both tests or not.

Jan

JamesKane
03-05-2019, 01:04 PM
A bit early here, but do folk somehow join their BigY and WGS results for the Y part together in a larger BAM.

I've done some similar experiments to this using a Y Elite 1.0 and YSEQ 30x WGS. Basically, the reverse of what you are considering. Adding a 100 base pair targeted test into a 150 base pair WGS result.

Use a tool like AddOrReplaceReadGroups on both BAMs to make sure they have the same read group sample name. Then use "samtools merge out.bam bigy.bam dante.bam". I don't recall if a sort was in order after this point.

Caveat: This assumes the source BAMs are aligned to the same reference and contigs match order. If not, you will need to revert both to FASTQ and realign. Expect to loose 48 to 95 hours of your computing resources while doing that. :) Somewhere in this thread I linked to a blog post and some gists over on Github to do it.

The reason I abandoned looking at this any further is the CallableLoci metric in the result was lower than the YSEQ 30x WGS BAM on it's own. I found it more beneficial to joint genotype the samples and reject the conflicting call sites.

MacUalraig
03-05-2019, 02:22 PM
The reason I abandoned looking at this any further is the CallableLoci metric in the result was lower than the YSEQ 30x WGS BAM on it's own.

Why was that?

JamesKane
03-05-2019, 04:26 PM
The cause is largely due to 100 base pair reads having lower mapping quality scores in regions the 150 base pair reads span better. Since the callable loci metric rejects regions where more than 10% of the reads fall below threshold, those 100 base pair reads lower the score.

We could also be seeing PCR stutter artifacts in that, but since there was no gain in useful information I stopped looking at the approach.

MacUalraig
03-05-2019, 05:04 PM
Excitement - my Dante VCF has finally arrived! Downloaded and having a look in IGV against my old hg19 wgs I did a while back and my original hg19 Y Elite.

Will have to go and order the BAM now I guess. :-)

To recap
17.7.18 ordered
25.7.18 back to lab
27.8.18 passed QA
5.3.19 snp and indel VCFs available for download

MacUalraig
03-05-2019, 07:09 PM
Just had a quick look at the most local Y SNPs. Overall Dante had the same or better depth than both FGC Y Elite 1.0 and YSEQx30. The downside is that four key SNPs are missing from the VCF that were read by the other two labs, two branch equivalents FGC4078 and FGC4087 and two of my local SNPs FGC5870 and FGC5873 (palindrome). That is 4 missing from 20 key SNPs checked. Of course they might be lurking in the BAM when I get it.

pmokeefe
03-05-2019, 07:33 PM
Just had a quick look at the most local Y SNPs. Overall Dante had the same or better depth than both FGC Y Elite 1.0 and YSEQx30. The downside is that four key SNPs are missing from the VCF that were read by the other two labs, two branch equivalents FGC4078 and FGC4087 and two of my local SNPs FGC5870 and FGC5873 (palindrome). That is 4 missing from 20 key SNPs checked. Of course they might be lurking in the BAM when I get it.
For the raw data, did you request that on hard drive or it it supposed to be downloadable? If hard drive, was there an extra charge?

MacUalraig
03-05-2019, 08:24 PM
For the raw data, did you request that on hard drive or it it supposed to be downloadable? If hard drive, was there an extra charge?

There was a link to where you could order it as a product but I can't find it... so I'll have to email. I can't download that big a file with my ISP deal anyway so it has to be a disk.

Helves
03-05-2019, 08:28 PM
Whole Genome Sequence with mtDNA for 199.00 with discount code: JUSTFORME199

Offer only valid until Sunday 17th February

This discount code is still working. I ordered mine today.

MacUalraig
03-06-2019, 08:30 AM
This is the link again for ordering the BAM, it costs e59.00

https://www.dantelabs.com/products/500-gb-hard-disk-containing-your-raw-data

bjp
03-06-2019, 02:40 PM
Whole Genome Sequence with mtDNA for 199.00 with discount code: JUSTFORME199

Offer only valid until Sunday 17th February

I see the post before mine stated that this discount code is still active.

Just adding one bit of information: for the Dante kit that I have been working with, which was ordered as the WGS product from Amazon on Prime Day, had ZERO records in the VCF file mapped to mitochondrial DNA. Once I receive the BAM, I expect to be able to pull out mtDNA reads, but in the meantime anyone wanting mtDNA calls may want to focus on ordering a product that specifically calls out the return of mtDNA results like this one above does.

ntk
03-07-2019, 03:00 PM
I see the post before mine stated that this discount code is still active.

Just adding one bit of information: for the Dante kit that I have been working with, which was ordered as the WGS product from Amazon on Prime Day, had ZERO records in the VCF file mapped to mitochondrial DNA. Once I receive the BAM, I expect to be able to pull out mtDNA reads, but in the meantime anyone wanting mtDNA calls may want to focus on ordering a product that specifically calls out the return of mtDNA results like this one above does.

This shouldn't surprise anyone but I just tried this code on the US site and it doesn't work. I did get an order in in February and the returned kit was confirmed "delivered to the garage or an alternate location at the address at 3:39 pm on February 25, 2019 in DRAPER, UT 84020."

Sadly the status is still unchanged as "Waiting confirmation from Dante Labs". I suppose others in my cohort are still waiting on acknowledgment too? I'm in it for the long haul, as long as they don't go bankrupt and I get my results in the next year or so I'll be okay with that.

aaronbee2010
03-07-2019, 03:10 PM
This shouldn't surprise anyone but I just tried this code on the US site and it doesn't work. I did get an order in in February and the returned kit was confirmed "delivered to the garage or an alternate location at the address at 3:39 pm on February 25, 2019 in DRAPER, UT 84020."

Sadly the status is still unchanged as "Waiting confirmation from Dante Labs". I suppose others in my cohort are still waiting on acknowledgment too? I'm in it for the long haul, as long as they don't go bankrupt and I get my results in the next year or so I'll be okay with that.

My status remains at "Waiting confirmation at Dante Labs" as well. I know from tracking that they received my kit on Friday 1st March, and the name of the person who signed for the parcel was the same person on the labels of the parcel shipped to me and the parcel shipped back to Dante Labs. I'm considering sending them an email if the status doesn't change within a week.

The only explanation on their part I can think of is that they deal with kits in batches as opposed to individually?

I did buy this knowing it would take up to a year to see my results though.

Also, the code only works on the EU site however, US users can use a VPN to access the EU site and make an order with that discount code.

Tonev
03-14-2019, 06:33 PM
Right, I have today picked up the HDD with my raw data from DHL (after kit ordered in mid-August 2018, kit delivered in Rome in Sept-2018, VCF file provided online in Dec-2018 plus explicit order for including me in HDD queue.... HDD received ~15 weeks after that).
There are several folders with various files with totally of ~235 Gb. First of all- I can see the bam file, but no file with extention fastq...
Here anyone with experience would be of great hep for me. I can upload folders screenshots if needed.
So question one: which would be the extention /name of the fastq file.
Question two: As far as YFULL accepts online link only to raw data files, any ideas about cloud data storage of 115 to 240 Gb, preferably for cost-effective and shorter period of time?

MacUalraig
03-14-2019, 07:01 PM
They should be hard to miss due to their size, my YSEQ ones are gzipped but inside the zip they are .fastq

Sample_wgs-S582Nr65_skewertemp-trimmed-pair2.fastq is one.

I have two as they are paired end and size around 21Gb zipped each.

E:\37\fastq>dir
Volume in drive E has no label.

Directory of E:\37\fastq

11/02/2019 11:23 <DIR> .
11/02/2019 11:23 <DIR> ..
07/02/2019 17:07 21,110,731,423 37_R1.fastq.gz
07/02/2019 17:10 22,246,362,628 37_R2.fastq.gz
2 File(s) 43,357,094,051 bytes
2 Dir(s) 47,915,073,536 bytes free

:\ :\ :\ :-)

MacUalraig
03-14-2019, 07:05 PM
For YFull I would extract a Y only BAM using samtools and just upload that rather than the whole thing. Stick it on google drive or equivalent and send them a share to it.

Something like:

samtools view ginormous.bam chrY -b > YFull_y.bam

pmokeefe
03-14-2019, 10:01 PM
Right, I have today picked up the HDD with my raw data from DHL (after kit ordered in mid-August 2018, kit delivered in Rome in Sept-2018, VCF file provided online in Dec-2018 plus explicit order for including me in HDD queue.... HDD received ~15 weeks after that).
There are several folders with various files with totally of ~235 Gb. First of all- I can see the bam file, but no file with extention fastq...
Here anyone with experience would be of great hep for me. I can upload folders screenshots if needed.
So question one: which would be the extention /name of the fastq file.
Question two: As far as YFULL accepts online link only to raw data files, any ideas about cloud data storage of 115 to 240 Gb, preferably for cost-effective and shorter period of time?
I received my Hard Drive with raw data from Dante Labs back in July, 2018.
There were 8 pairs of fastq files, e.g.
CL100065945_L02_562_1.fq.gz
CL100065945_L02_562_2.fq.gz

Tonev
03-14-2019, 10:49 PM
I received my Hard Drive with raw data from Dante Labs back in July, 2018.
There were 8 pairs of fastq files, e.g.
CL100065945_L02_562_1.fq.gz
CL100065945_L02_562_2.fq.gz

Any advise on sources for their interpretation?