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Johnny ola
12-24-2020, 06:26 PM
My Greek friend ordered one kit at 26/11. The delivery and the return of the sample went very smoothly and today, after aprox. a week and a half in the "awaiting qc inspection" stage, his sample continued to "sequencing started" . How much will he have to wait, in the best case scenario and also at normal circumastances, for his results to be ready ? A member of the facebook group who also ordered a normal 8 weeks kit at 26/11 got freakishly lucky and got his results today :eek: ! But cases like his must be one in a million...obviously I don't expect similar timeframes.

I was about to order a kit for my grandma but i cancel it....

lacreme
12-24-2020, 06:38 PM
I was about to order a kit for my grandma but i cancel it....

Was it due to their iffy at best reputation ?
Well my friend might not have taken the risk at 260 euros that's currently selling for but for 150 (less in reality as he used a vpn to get the us price) back then he couldn't resist it :D

Jatt1
12-24-2020, 07:35 PM
I didnt update, but I received my kit 1 week after I ordered it on black friday.

I ordered on 24/11 and haven't received the kit yet.

Johnny ola
12-24-2020, 07:41 PM
Was it due to their iffy at best reputation ?
Well my friend might not have taken the risk at 260 euros that's currently selling for but for 150 (less in reality as he used a vpn to get the us price) back then he couldn't resist it :D

What we live.... :rofl:

I wanted badly to order a kit For my grandma. She Is 82 and I am In a hurry... I hope This joke with covid to come to an End...

lacreme
12-24-2020, 08:37 PM
What we live.... :rofl:

I wanted badly to order a kit For my grandma. She Is 82 and I am In a hurry... I hope This joke with covid to come to an End...

The next cheapest option seems to be the kit from sequencing. 100$ more but possibly without the need of a subscription, unlike Nebula's

MacUalraig
12-24-2020, 08:49 PM
The next cheapest option seems to be the kit from sequencing. 100$ more but possibly without the need of a subscription, unlike Nebula's

"Silver Membership is $11.99 per month ($9.99 if paid annually) and provides the ability to select and use two DNA analysis apps and reports each month. View additional information about Membership Plans.

The current promotion for our Ultimate DNA Test and our Ultimate Genome Sequencing service includes a free month of Silver Membership."
"You can cancel your Membership at any time and for any reason without incurring any fee or penalty."

In which case not much difference from buying via Nebula, just make sure you remember to cancel the future payments.

dosas
12-24-2020, 10:06 PM
The next cheapest option seems to be the kit from sequencing. 100$ more but possibly without the need of a subscription, unlike Nebula's

Sequencing.com is a reseller for Nebula, don't trust them as they have terrible customer support.

crazyladybutterfly
12-30-2020, 04:06 PM
Last year I used their service and got my data in 2 weeks but I live in italy.

Jatt1
01-02-2021, 06:02 AM
Last year I used their service and got my data in 2 weeks but I live in italy.

Ordered on Nov. 24th, haven't received the kit yet .

MacUalraig
01-05-2021, 12:31 PM
The UK edition of the Dante site is offering wgs for 259 via the checkout code RESOLUTION2021... ;-)

ThaYamamoto
01-08-2021, 05:22 PM
Anyone have any idea when their next sale might be? I was hoping over boxing day/the new year but it never happened. Missed the last one.

Ibericus
01-08-2021, 06:22 PM
Dante and Yfull should partner together. They should sell an all-inclusive product to compete with the (future) Nebula-FTDNA partnership.

MacUalraig
01-08-2021, 06:29 PM
Various people including myself asked them to do an easy YFull upload option and they said they would but don't think it ever materialised. But YFull needs to stay independent of any vendor IMHO.

hartaisarlag
01-08-2021, 06:32 PM
Various people including myself asked them to do an easy YFull upload option and they said they would but don't think it ever materialised. But YFull needs to stay independent of any vendor IMHO.

YSEQ's bridge service was very helpful for this; they initiated a transfer within <48 hours.

teepean47
01-08-2021, 09:16 PM
Dante and Yfull should partner together. They should sell an all-inclusive product to compete with the (future) Nebula-FTDNA partnership.

YFull is already cooperating with Yseq.

Jatt1
01-08-2021, 10:09 PM
YFull is already cooperating with Yseq.

Yseq services are great but it might be more expensive than Dante Labs and Nabula Genomics.

Ibericus
01-09-2021, 06:52 AM
Various people including myself asked them to do an easy YFull upload option and they said they would but don't think it ever materialised. But YFull needs to stay independent of any vendor IMHO.

That's the thing. I have read several comments of people who are put off from doing a WGS test not because of the cost (~$300) but because of the technical difficulties they may face. I think there's room for expansion at these prices if it were just a little easier.

Jatt1
01-09-2021, 07:22 AM
That's the thing. I have read several comments of people who are put off from doing a WGS test not because of the cost (~$300) but because of the technical difficulties they may face. I think there's room for expansion at these prices if it were just a little easier.

YSEQ will take care of those technical difficulties for a nominal fee.

Jatt1
01-09-2021, 07:26 AM
Dante and Yfull should partner together. They should sell an all-inclusive product to compete with the (future) Nebula-FTDNA partnership.

Do you still see that there are any chances of a partnership deal between FTDNA and Nebula Genomics?

teepean47
01-09-2021, 08:19 AM
Yseq services are great but it might be more expensive than Dante Labs and Nabula Genomics.

Way too expensive compared to Dante and Nebula.

Ibericus
01-09-2021, 08:51 AM
Do you still see that there are any chances of a partnership deal between FTDNA and Nebula Genomics?

I don't know. When I received Nebula's kit I saw that it had FTDNA labels and the return address was the same so I figured it was a spin-off company of some kind. Because of that I always thought the partnership was the next logical step. But maybe they just provide the kits and then they forward them to Asia, I don't know.

Jatt1
01-09-2021, 09:02 AM
Way too expensive compared to Dante and Nebula.

WGS yes, but SNP tests are cheap and so is converting Dante Labs etc. HG 37 BAM file to HG38.

MacUalraig
01-09-2021, 09:22 AM
I don't know. When I received Nebula's kit I saw that it had FTDNA labels and the return address was the same so I figured it was a spin-off company of some kind. Because of that I always thought the partnership was the next logical step. But maybe they just provide the kits and then they forward them to Asia, I don't know.

IIRC Houston extracts the DNA then its off to BGI. My concern is mostly about what happens afterwards, how certain can we be that Houston doesn't have access to the sequenced data (especially bearing in mind their forensic services).

A full partnership never made sense to me since who would waste time buying BY from then on? On the other hand they do MyHeritage tests for them and MH has way overtaken FF in database size. Maybe they are realising finally that these arrangements aren't such a good idea.

ChrisR
01-19-2021, 02:06 PM
I have not followed DL closely in the last year or so.

Currently when with an Italian provider I navigate to dantelabs.com it redirects me to dantelabs.it with only Italian language content. Under "Test del DNA" (URL is "advanced-dna-tests") I get redirected to "Pagina non trovata" (Page not found). The main site seems to run on the Shopify system while the login "Il mio account" redirects to genome.dantelabs.com where the personal data of existing kits can be accessed (tried).
Earlier I was able to get to a page for the Human Genome Sequencing which stated "Da Settembre i nostri Test avanzati del DNA saranno venduti in esclusiva da Anima Genomics (https://www.animagenomics.com/)" (from September our advanced DNA tests are sold exclusively by Anima Genomics).
42690
On the Anima Genomics site also only in Italian while two Tests GOLD and PLATINUM are presented, no detailed description, prices and order possibility seems available.
42691

With a VPN and non-Italian-IP or from outside Italy you stay on the dantelabs.com site and when ordering WGS30x ($599 with code discounted to $259) you can select also Italy as shipping country and continue to the payment checkout page. As Анна А. on the facebook group stated she wanted to order from/to Italy and DL responded her via email that for Italy only Animagenomics is operative.

So not sure about the situation and why DanteLabs would operate from L'Aquila in Italy, sell Sequencing internationally but not domestically?
Since on the .com site you can order with shipping to Italy I'm not sure if they cancel such orders?

Jatt1
01-20-2021, 05:56 AM
I have not followed DL closely in the last year or so.

Currently when with an Italian provider I navigate to dantelabs.com it redirects me to dantelabs.it with only Italian language content. Under "Test del DNA" (URL is "advanced-dna-tests") I get redirected to "Pagina non trovata" (Page not found). The main site seems to run on the Shopify system while the login "Il mio account" redirects to genome.dantelabs.com where the personal data of existing kits can be accessed (tried).
Earlier I was able to get to a page for the Human Genome Sequencing which stated "Da Settembre i nostri Test avanzati del DNA saranno venduti in esclusiva da Anima Genomics (https://www.animagenomics.com/)" (from September our advanced DNA tests are sold exclusively by Anima Genomics).
42690
On the Anima Genomics site also only in Italian while two Tests GOLD and PLATINUM are presented, no detailed description, prices and order possibility seems available.
42691

With a VPN and non-Italian-IP or from outside Italy you stay on the dantelabs.com site and when ordering WGS30x ($599 with code discounted to $259) you can select also Italy as shipping country and continue to the payment checkout page. As Анна А. on the facebook group stated she wanted to order from/to Italy and DL responded her via email that for Italy only Animagenomics is operative.

So not sure about the situation and why DanteLabs would operate from L'Aquila in Italy, sell Sequencing internationally but not domestically?
Since on the .com site you can order with shipping to Italy I'm not sure if they cancel such orders?

I ordered a kit on Nov. 24th 2020 and haven't received it yet.

Arlus
01-20-2021, 07:19 AM
I ordered a kit on Nov. 24th 2020 and haven't received it yet.

Have you contacted the postal service yet? It should have arrived by now.

Jatt1
01-20-2021, 07:27 AM
Have you contacted the postal service yet? It should have arrived by now.

no further information.
Delivery status
Expected delivery: Tuesday, Jan. 19, 8:30 am to 12:30 pm Help
Delivery details
Origin
Plattling, DE
In transit
Jan. 19
Received by Canada Post
Jan. 4
Expected delivery
Jan. 19,
8:30 am to 12:30 pm

They changed the delivery date from 15th to 19th but didn't deliver. Did you get yours?

Arlus
01-20-2021, 08:27 AM
no further information.
Delivery status
Expected delivery: Tuesday, Jan. 19, 8:30 am to 12:30 pm Help
Delivery details
Origin
Plattling, DE
In transit
Jan. 19
Received by Canada Post
Jan. 4
Expected delivery
Jan. 19,
8:30 am to 12:30 pm

They changed the delivery date from 15th to 19th but didn't deliver. Did you get yours?
Yeah, I received mine but it took around 40 days to arrive. The delay in my case was most probably due to COVID related backlog of Indiapost. Maybe you should try contacting directly to the respective international sorting center.

Jatt1
01-20-2021, 08:51 AM
Yeah, I received mine but it took around 40 days to arrive. The delay in my case was most probably due to COVID related backlog of Indiapost. Maybe you should try contacting directly to the respective international sorting center.

DHL stuff here in Canada is handled by Canada Post in certain cases, I think they might have either misplaced it or lost it somehow. Just look at the update by Canada Post, In transit Jan. 20, Expected delivery Jan. 19, 8:30 am to 12:30 pm

Origin
Plattling, DE
In transit
Jan. 20
Received by Canada Post
Jan. 4
Expected delivery
Jan. 19,
8:30 am to 12:30 pm

Arlus
01-20-2021, 09:53 AM
DHL stuff here in Canada is handled by Canada Post in certain cases, I think they might have either misplaced it or lost it somehow. Just look at the update by Canada Post, In transit Jan. 20, Expected delivery Jan. 19, 8:30 am to 12:30 pm

Origin
Plattling, DE
In transit
Jan. 20
Received by Canada Post
Jan. 4
Expected delivery
Jan. 19,
8:30 am to 12:30 pm

You can ask Dantelabs to send you a new kit.

tgndjs
01-20-2021, 01:54 PM
I got my results today (much sooner than I anticipated) but I have to say... I am quite disappointed with the average read depth of mine.

42710

As you can see, my average read depth is only 23x.... which is way lower than what Dante Labs promised(30x)
Is this normal for Dante Labs or should I file a complaint?

I've done a 30x WGS from Nebula before and I got 33x from them.

Here's my results from Nebula to compare.
42711

Kazakh
01-20-2021, 03:08 PM
I got my results today (much sooner than I anticipated) but I have to say... I am quite disappointed with the average read depth of mine.

42710

As you can see, my average read depth is only 23x.... which is way lower than what Dante Labs promised(30x)
Is this normal for Dante Labs or should I file a complaint?

I've done a 30x WGS from Nebula before and I got 33x from them.

Here's my results from Nebula to compare.
42711

Really sad to see that:-( Did you buy a Dante kit during the last Black Friday sales?
They sell 90gigabases before mapping,so they would probably refuse to resequence extra(

MacUalraig
01-20-2021, 04:08 PM
I got my results today (much sooner than I anticipated) but I have to say... I am quite disappointed with the average read depth of mine.

42710

As you can see, my average read depth is only 23x.... which is way lower than what Dante Labs promised(30x)
Is this normal for Dante Labs or should I file a complaint?

I've done a 30x WGS from Nebula before and I got 33x from them.

Here's my results from Nebula to compare.
42711

It can be annoying I know but another way of looking at your results is how good (reliable) are the critical calls? I regularly use a 15x WGS for Y testing without any problems so far. If there is a SNP you want and it needs retesting that's another matter of course.

tgndjs
01-21-2021, 08:37 AM
Yeah, I bought it last Black Friday day, so it was much cheaper than Nebula(only half the price) yet it's still bit disappointing for sure.
I mean... I wonder why there is such a big difference in mapped reads between them (Dante 80% vs Nebula 99%)

lacreme
01-21-2021, 10:21 AM
Yeah, I bought it last Black Friday day, so it was much cheaper than Nebula(only half the price) yet it's still bit disappointing for sure.
I mean... I wonder why there is such a big difference in mapped reads between them (Dante 80% vs Nebula 99%)

Hi! when did your kit started sequencing? And at which lab (if they have more than one) ? A friend also bought a kit during the black friday sales and it started sequencing at the Italian lab in 24/12. He doesn't have his results yet, and due to the seemingly random times at which they process the kits he doesn't have a specific timeframe in his mind, but he is interested in feedback from people who ordered one in close dates nonetheless.

Kazakh
01-21-2021, 10:42 AM
Yeah, I bought it last Black Friday day, so it was much cheaper than Nebula(only half the price) yet it's still bit disappointing for sure.
I mean... I wonder why there is such a big difference in mapped reads between them (Dante 80% vs Nebula 99%)

Sure, it feels like a ripoff when you pay for 30x and get 23x in return. But this is Dante Labs' business model! They countless times replied to customers, that they sell 90 gigabases before mapping.

But for price of 149$ 23x looks not so bad. For mapped gigabases per $ it is better than Nebula:imho

Any plans to send raw data for YFull this time? You might get better coverage and more STR results with this result than with Nebula. Give it a try.

Since YSeq sells 15x (at 599$), results like yours are useable nonetheless.

Regarding the difference in mapping %, it depends on many factors. How well sample submitted was collected, how it handled at laboratory and so on. Generally speaking, buccal swabs yields better WGS mapped coverage than saliva. The latter one is prone to be a medium for a variety of bacteria types. Blood samples is even better than buccal swabs.

tgndjs
01-21-2021, 12:13 PM
Hi! when did your kit started sequencing? And at which lab (if they have more than one) ? A friend also bought a kit during the black friday sales and it started sequencing at the Italian lab in 24/12. He doesn't have his results yet, and due to the seemingly random times at which they process the kits he doesn't have a specific timeframe in his mind, but he is interested in feedback from people who ordered one in close dates nonetheless.

Ummm... I know nothing about their lab. All I know is that mine got shipped to L'Aquila according to the shipping label.

Anyhow here's my brief timeline

purchased on Black Friday, 2020
Delievered on Dec 7, 2020
Registered/shipped back to the lab on Dec 22, 2020
Arrived at the lab (according to DHL) on Dec 24, 2020
Status changed to "We Received Your Kit" on Dec 28, 2020
Status changed to "Sequencing Started" on Jan 14, 2021
Got my results yesterday Jan 20, 2021

Hope this helps!

tgndjs
01-21-2021, 12:31 PM
Sure, it feels like a ripoff when you pay for 30x and get 23x in return. But this is Dante Labs' business model! They countless times replied to customers, that they sell 90 gigabases before mapping.

But for price of 149$ 23x looks not so bad. For mapped gigabases per $ it is better than Nebula:imho

Any plans to send raw data for YFull this time? You might get better coverage and more STR results with this result than with Nebula. Give it a try.

Since YSeq sells 15x (at 599$), results like yours are useable nonetheless.

Regarding the difference in mapping %, it depends on many factors. How well sample submitted was collected, how it handled at laboratory and so on. Generally speaking, buccal swabs yields better WGS mapped coverage than saliva. The latter one is prone to be a medium for a variety of bacteria types. Blood samples is even better than buccal swabs.

Really? 90 Gbases before mapping? that's something I was not aware of :)
Yeah, in terms of money, it's not bad; as you said I got 23x for the price of $149. But it would've been nice if I had known that 30x means 90 Gbases for Dante Labs.
I was bit confused when I got the results as the average read depth was significantly lower than that of Nebula when both companies claims same 30x WGS service.

I am not going to upload this one to YFull. Recently, I've purchased another WGS kit from Nebula to get my father tested. I will upload his when the it becomes available.

Kazakh
01-21-2021, 12:48 PM
Really? 90 Gbases before mapping? that's something I was not aware of :)

Quote from their Customer Service for cases similar to yours:
"Our policy is to only resequence samples when they are less than our specifications of 90 gigabases."

lacreme
01-21-2021, 01:00 PM
Ummm... I know nothing about their lab. All I know is that mine got shipped to L'Aquila according to the shipping label.

Anyhow here's my brief timeline

purchased on Black Friday, 2020
Delievered on Dec 7, 2020
Registered/shipped back to the lab on Dec 22, 2020
Arrived at the lab (according to DHL) on Dec 24, 2020
Status changed to "We Received Your Kit" on Dec 28, 2020
Status changed to "Sequencing Started" on Jan 14, 2021
Got my results yesterday Jan 20, 2021

Hope this helps!

At L'aquila indeed, that's what I originally meant but I had forgotten the place.

2 or 8 weeks kit ?

tgndjs
01-21-2021, 01:05 PM
At L'aquila indeed, that's what I originally meant but I had forgotten the place.

2 or 8 weeks kit ?

It was an 8 weeks kit though it took less than that.

lacreme
01-21-2021, 01:39 PM
It was an 8 weeks kit though it took less than that.

:eek: !

Your results may not have been 30x but other than that you were definitely very lucky then. Imagine having to wait for almost a year and getting suboptimal results in the end like it have happened many times before (reading comments online) ...

I just hope that my friend who also bought a 8 weeks kit won't be one such case :biggrin1:

ChrisR
01-28-2021, 02:18 PM
dna-warehouse reports 13x as median Y-coverage for ca. 70 DL samples. What might be the top 10% value of those kits? 16-17x? At least in the other direction I saw a lot of chrY DL results with coverage of only 10x or even lower.

MacUalraig
01-28-2021, 03:08 PM
dna-warehouse reports 13x as median Y-coverage for ca. 70 DL samples. What might be the top 10% value of those kits? 16-17x? At least in the other direction I saw a lot of chrY DL results with coverage of only 10x or even lower.

James should distinguish between the Dante-China and Dante-Italy runs for clarity. My short read test from Dante was done at BGI and very good, the Italian ones less so from what I can see.

ssamlal
01-28-2021, 06:54 PM
I bought an 8 week 30x kit for my maternal uncle during their last sale. Got the results back before 8 weeks but very disappointed.

The average read depth is 24x, mapped Gbases 77.37 and raw Gbases 82.53 (as reported in WGS Extract).

I reached out to Dante Labs since raw Gbases was less than 90. Their response was: "According to our internal records, your sample received 93,36 gigabases, therefore it does not qualify for resequencing."

42912

Jatt1
01-28-2021, 07:05 PM
I bought an 8 week 30x kit for my maternal uncle during their last sale. Got the results back before 8 weeks but very disappointed.

The average read depth is 24x, mapped Gbases 77.37 and raw Gbases 82.53 (as reported in WGS Extract).

I reached out to Dante Labs since raw Gbases was less than 90. Their response was: "According to our internal records, your sample received 93,36 gigabases, therefore it does not qualify for resequencing."

42912

I too bought a kit but haven't sent it back yet, surely bad news in your case.

ssamlal
01-29-2021, 01:17 PM
I bought an 8 week 30x kit for my maternal uncle during their last sale. Got the results back before 8 weeks but very disappointed.

The average read depth is 24x, mapped Gbases 77.37 and raw Gbases 82.53 (as reported in WGS Extract).

I reached out to Dante Labs since raw Gbases was less than 90. Their response was: "According to our internal records, your sample received 93,36 gigabases, therefore it does not qualify for resequencing."

42912

I pushed them to check again and got this response. Stay tuned.

42945

ssamlal
02-02-2021, 11:39 AM
I pushed them to check again and got this response. Stay tuned.

42945

Updated file stats:

43012

Arlus
02-25-2021, 01:12 PM
Has anyone contacted Dante Labs customer support recently? They have stopped answering my emails altogether.
Their DHL return label was not available at my address, so I had to use Indiapost for sending back my sample. Unfortunately it got held in customs for 'incomplete documentation' on 5th February. Initially they were responsive and were helping and they had told that they were waiting to be contacted by Poste Italiane. But I have not heard from them since then.
Poste Italiane twitter has suggested me to wait for further updates. Most of the their contact numbers are unavailable and the one available has no English speakers.

MacUalraig
02-25-2021, 02:07 PM
Has anyone contacted Dante Labs customer support recently? They have stopped answering my emails altogether.
Their DHL return label was not available at my address, so I had to use Indiapost for sending back my sample. Unfortunately it got held in customs for 'incomplete documentation' on 5th February. Initially they were responsive and were helping and they had told that they were waiting to be contacted by Poste Italiane. But I have not heard from them since then.
Poste Italiane twitter has suggested me to wait for further updates. Most of the their contact numbers are unavailable and the one available has no English speakers.

Have you tried their official support fb group? It can help although by no means guaranteed.

Arlus
02-25-2021, 02:16 PM
Have you tried their official support fb group? It can help although by no means guaranteed.

Thanks, I will try that.

teepean47
02-26-2021, 05:59 AM
Thanks, I will try that.

Giving them a poor Trustpilot review is also a good method.

Arlus
02-26-2021, 06:39 AM
Giving them a poor Trustpilot review is also a good method.

Yeah, I am currently waiting to get accepted into their Facebook support group. If that fails then I will try trustpilot and bbb.

MacUalraig
02-26-2021, 09:08 AM
Quotes from the aforementioned group:

"Customer service is currently receiving an overwhelming amount of emails and is doing their best to reply to everyone in a timely manner."
"Due to the high volume of messages, it may take 3-5 business days to receive a reply, sorry about this and thank you for your patience!" (22h ago)

Arlus
02-26-2021, 09:11 AM
Quotes from the aforementioned group:

"Customer service is currently receiving an overwhelming amount of emails and is doing their best to reply to everyone in a timely manner."
"Due to the high volume of messages, it may take 3-5 business days to receive a reply, sorry about this and thank you for your patience!" (22h ago)

I hope that they will reply this time.

ssamlal
02-28-2021, 07:28 PM
I did two 30x WGS tests (both at Dante Labs). The BAM file that I downloaded for one test was gzipped (the other was not). After unzipping it (using 7-Zip) the size was 238 GB. This seems unusually large given that my other BAM file was 52.4 GB.

It looks like the files are no longer available for download (archived). Thoughts anyone?

43605

43606

aaronbee2010
02-28-2021, 10:47 PM
I did two 30x WGS tests (both at Dante Labs). The BAM file that I downloaded for one test was gzipped (the other was not). After unzipping it (using 7-Zip) the size was 238 GB. This seems unusually large given that my other BAM file was 52.4 GB.

It looks like the files are no longer available for download (archived). Thoughts anyone?

43605

43606

Try changing the extension of the ".gz" file to ".bam" and see if WGSExtract generates a ".bai" index file when you load the BAM file in the program. If that works without any issues being printed in the WGSExtract console, then it turns out that you've been given a BAM file with a wrong extension. This has been an issue that Dante has been known for well over a year ago, so it's surprising to see that it's happened again. Having said that, your specific instance seems to be isolated considering that I haven't seen the issue come up recently on the two main Facebook groups where Dante Labs customer write about their issues.

Also, if you don't download your raw data within 90 days of it becoming available for the first time, the data gets migrated to cold storage (cheaper for Dante Labs to pay for but not instantly accessible) which then needs a silver or gold subscription to be purchased (for each kit) before Dante Labs will re-migrate the data to regular storage which is instantly accessible (can be downloaded from). This shouldn't happen before that 90 day cut-off but again, this has happened to some customers and you would have to contact their customer support to get this issue resolved.

Jatt1
02-28-2021, 11:09 PM
I did two 30x WGS tests (both at Dante Labs). The BAM file that I downloaded for one test was gzipped (the other was not). After unzipping it (using 7-Zip) the size was 238 GB. This seems unusually large given that my other BAM file was 52.4 GB.

It looks like the files are no longer available for download (archived). Thoughts anyone?

43605

43606

Does this 238 GB file belongs to 100X test?

aaronbee2010
02-28-2021, 11:25 PM
Does this 238 GB file belongs to 100X test?

BAM files themselves are bgzip compressed. Uncompressing them will produce a file around 6-8 times larger, like what's happened here.

ssamlal
03-01-2021, 12:55 AM
Thank you @aaronbee! It worked. I can't believe I didn't think of that, LOL

43611

lacreme
03-10-2021, 11:57 AM
My Greek friend just got his WGS hg19 results (after approximately 3 months, not too bad... ) and he is now waiting for the paid hg38 upgrade from Dante Labs.

A first question, provided his data has good enough coverage (haven't finished downloading to check with qual iobio io ) what is the best format to use for autosomal extraction and for use with Ydna/Mtdna tools respectively ? I think I recall a mention/post either here or on the unofficial facebook group that hg19 is better for autosomal and hg38 for the other uses ? Or am I misremembering ?

Arlus
03-19-2021, 12:30 PM
An update regarding my situation: my sample was finally released from customs and has reached to the labs.

trdbr1234
03-20-2021, 10:24 PM
3 Months already and still in "Sequencing Started". Is the average turnaround 3-4 months? Or are there Covid related delays in play here?

Arlus
04-17-2021, 01:32 PM
Is it recommended to realign to hg38 before uploading to Yfull?
My computer is probably too weak for running those programs. So the options available to me are- sequencing.com, yseq, realignment by Dante labs themselves and if I am correct yfull offers upgradation to hg38 too.
Which option should I choose?

MacUalraig
04-17-2021, 03:52 PM
Is it recommended to realign to hg38 before uploading to Yfull?
My computer is probably too weak for running those programs. So the options available to me are- sequencing.com, yseq, realignment by Dante labs themselves and if I am correct yfull offers upgradation to hg38 too.
Which option should I choose?

How much RAM does your computer have? I have done alignment on an 8Gb machine but it wouldn't run on my old 4Gb laptop. At least under windows which has a lot of overhead.

Arlus
04-17-2021, 05:25 PM
How much RAM does your computer have? I have done alignment on an 8Gb machine but it wouldn't run on my old 4Gb laptop. At least under windows which has a lot of overhead.

Unfortunately it's just 4gb & an i3.

Arlus
06-02-2021, 01:20 AM
44916

Timeline-
Kit shipped to me - 25th Nov 2020
Kit received- 3rd Jan 2021
Kit shipped back- 11th Jan 2021
Kit received at the lab- 22nd March 2021 (delay due to customs issues)
Sequencing started- 16th April 2021
Results ready- 26th May 2021

aaronbee2010
06-02-2021, 02:34 PM
44916

Timeline-
Kit shipped to me - 25th Nov 2020
Kit received- 3rd Jan 2021
Kit shipped back- 11th Jan 2021
Kit received at the lab- 22nd March 2021 (delay due to customs issues)
Sequencing started- 16th April 2021
Results ready- 26th May 2021

I don't think I've ever seen a Dante Labs BAM reach the 50x mapped mark before. Congratulations!

Arlus
06-02-2021, 03:05 PM
I don't think I've ever seen a Dante Labs BAM reach the 50x mapped mark before. Congratulations!

Thanks!
They probably oversequenced my sample.

aaronbee2010
06-02-2021, 10:45 PM
Thanks!
They probably oversequenced my sample.

They definitely did here. Their criteria for sufficiently sequencing a sample is 90 raw GBases, whereas your BAM has 179.

On another note, please consider backing up your raw data to another source (i.e. cloud storage or hard drive) as soon as you can as after 90 days, Dante Labs move your data to cold storage (cheaper for them to keep stored, but prevents you from downloading it unless you pay for a silver or gold subscription to move the data back to regular storage) and I've had issues on two different occasions with Dante Labs not moving all files back to regular storage (with the second issue still ongoing hence why I'm saying this, so you don't have to go through what I'm dealing with at the moment).

If you decide to go for AWS S3 storage (especially if you get the S3 bucket in the "eu-west-1" region, you can very quickly transfer all of your Dante Labs data (also located in an S3 bucket in the "eu-west-1" region) to your S3 bucket using an EC2 instance. When you make an AWS account, you can get a free EC2 instance (t2.micro) for a year but since these are cheap to rent for a small amount of time, I would consider renting an EC2 instance with download speeds of at least 1 gigabit. After this, you can optionally change the storage class of all files you've backed up to "Glacier". If you want to download the files again, you'll have to wait a bit, but Glacier storage is much cheaper than standard storage (you can store 1TB of data for only $4 a month with Glacier).

According to another Dante Labs customer, you can also request that Dante Labs send over the data directly to your S3 bucket themselves. Here's their comment:

https://i.gyazo.com/93e2b36bcb3cf222249c2928dc9fbe00.png

Only problem with this method that I can see is that you're at the mercy of Dante Labs customer support, whose responsiveness can be really inconsistent at times.

Arlus
06-03-2021, 03:31 AM
They definitely did here. Their criteria for sufficiently sequencing a sample is 90 raw GBases, whereas your BAM has 179.

On another note, please consider backing up your raw data to another source (i.e. cloud storage or hard drive) as soon as you can as after 90 days, Dante Labs move your data to cold storage (cheaper for them to keep stored, but prevents you from downloading it unless you pay for a silver or gold subscription to move the data back to regular storage) and I've had issues on two different occasions with Dante Labs not moving all files back to regular storage (with the second issue still ongoing hence why I'm saying this, so you don't have to go through what I'm dealing with at the moment).

If you decide to go for AWS S3 storage (especially if you get the S3 bucket in the "eu-west-1" region, you can very quickly transfer all of your Dante Labs data (also located in an S3 bucket in the "eu-west-1" region) to your S3 bucket using an EC2 instance. When you make an AWS account, you can get a free EC2 instance (t2.micro) for a year but since these are cheap to rent for a small amount of time, I would consider renting an EC2 instance with download speeds of at least 1 gigabit. After this, you can optionally change the storage class of all files you've backed up to "Glacier". If you want to download the files again, you'll have to wait a bit, but Glacier storage is much cheaper than standard storage (you can store 1TB of data for only $4 a month with Glacier).

According to another Dante Labs customer, you can also request that Dante Labs send over the data directly to your S3 bucket themselves. Here's their comment:

https://i.gyazo.com/93e2b36bcb3cf222249c2928dc9fbe00.png

Only problem with this method that I can see is that you're at the mercy of Dante Labs customer support, whose responsiveness can be really inconsistent at times.

Thanks! I didn't know about AWS, I will look into it. Downloading the BAM file was a real pain, with my connection it takes a minimum of 6 to 8 hours for downloading a 60gb file. Also, connection often gets interrupted. So, it took many tries for successfuly downloading the BAM file (stopped at 53, 57, 59 gbs LOL).
Right now, I am trying to download the fastq files.
I definitely will go for a backup, I hope that AWS is available in India.

MacUalraig
06-03-2021, 10:10 AM
Things seem to be on the move again with Dante although a lot of the comments at the start of this article are wrong and one of their employees has said you can still order via the US site using a VPN (!) pending 'changes underway' as per one of their staff on FB.

https://www.reddit.com/r/DanteLabs/comments/neuc1o/what_happened_to_dante_labs/

I'd be more specific if I knew.

hartaisarlag
08-21-2021, 04:17 AM
Anyone have experience making Y-SNP calls from their Dante .VCF files? I'm working on one, and none of the relevant positions (including for markers I'm sure this person is positive for) is showing up.

MacUalraig
08-21-2021, 06:45 AM
Anyone have experience making Y-SNP calls from their Dante .VCF files? I'm working on one, and none of the relevant positions (including for markers I'm sure this person is positive for) is showing up.

Are you checking hg19 or hg38 positions? With luck you should have a header entry telling you which the VCF is using like
##reference=file:///genomes/0/refseq/hg38/hg38.fa

or if in doubt check both versions for some of the markers.