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Thread: Dante Labs (WGS)

  1. #31
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    Maybe both then. The economist in me says the "hardcopy" should cost more, since as discussed, the better USB stick costs 60-90 EUR at my location, and DHL shipment to Italy looks to cost 40 EUR, so the expense that needs to be passed to customer is 100-130EUR, while as shown, one download serving from Amazon S3 is about 8 EUR. By all means, ask what is most convenient for you, especially if you can get it for free. Though given uploading the BAM online is bound to cost at least as much as downloading it, I think most people would still prefer to have at least a download link for YFull, FGC, Sequencing.com and what have you. In fact, I'd still wager most of their intended clientele can't process let alone upload 100G of data. Also, unless people are actually getting (or taking) free resources at work, school or home, doing your own analysis on cloud servers is bound to be more affordable thanks to economies of scale than using your own hardware (And currently free at Sequencing.com).

    Rant done

    Aside: YFull's "read count" and "unmapped reads" are identical to the numbers on the Dante Labs provided BAM, so if you *can* process the BAM file, I believe you can just extract the Y-chromosome part and save uploading most of it if you're doing *only* YFull (But better check with YFull first). Other services would require the whole file though.

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  3. #32
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    Quote Originally Posted by Donwulff View Post
    Aside: YFull's "read count" and "unmapped reads" are identical to the numbers on the Dante Labs provided BAM, so if you *can* process the BAM file, I believe you can just extract the Y-chromosome part and save uploading most of it if you're doing *only* YFull (But better check with YFull first). Other services would require the whole file though.
    I did that for a project member, it is quite trivial to split off a Y-only BAM using samtools.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  5. #33
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    samtools index original.bam
    samtools view -bo me_chrY_only.bam original.bam
    Of course, you need a fast computer running operating system with samtools etc. capable of reading USB sticks, preferably with 128GB or larger hard-drive. In other words, no phones or tablets. N.B. samtools doesn't allow you set compression level for view sub-command, and bam format is kinda wierd so it takes some gymnastics to re-compress; sort would let you but then you will need lots of memory and at least double the hard-drive. But the highest compression level doesn't save that much space, so it's probably not worth it.

    I re-mapped the Dante Labs BAM to GRCh38 (analysis ready + full decoy sets from bwa-kit) due in part to the talk about FTDNA switching to build 38, and the results did not change noticeably, read depths within one read of the original, or two reads for the one read YFull called "Low Quality". The GRCh38 chrY BAM has less reads total (including the unplaced contig), 10,527,139 vs. 12,090,138 for the Dante Labs provided build 37 one, so restricting the reads to chrY mapped probably doesn't hurt results too much even if they're re-analysed against build 38. Of course, the best would still be to run the whole original unfiltered BAM through the pipeline, but I don't know if even YFull is doing it.

    Removed reference to FTDNA's build 38 re-analysis; apparently they match, it's just that their "Non-matching variants" column lists both REF and ALT variants which don't match with the other person, which makes sense but isn't obvious.
    Last edited by Donwulff; 10-23-2017 at 12:15 PM.

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  7. #34
    Just wanted to say that I'm still waiting on results. I mailed my kit in on 8/4, so it's been over 12 weeks. When I originally contacted them a few weeks ago they said I'd have it by 10/20, then I contacted them again when that date came around and they're now saying 11/3.

    I asked if I could get the vcf as soon as it was available without having to wait for the report to be developed, and the person I was in contact with looked into it but unfortunately they can't do that, so I have to wait until everything is ready.

    I'm trying not to get too impatient because they're a new company and it was a ridiculously low price, but I'm really looking forward to getting my data.

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  9. #35
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    Did you get your results yet? I don't want to be recommending them if their delivery seems dodgy. As said mine was some weeks late too, but nothing drastic, and they shared a post from happy customer on Facebook, but otherwise I've heard little.
    As an aside, YFull updated my samples "Full Statistics" maybe a week ago to show 15 Novel SNP's for the Dante Labs sample. As I posted previously, this is the number of reliable novel SNP's found on my BigY test as well, so it would seem like in my case Dante Labs WGS doesn't improve over BigY results. I have no idea of YFull's methodology though, the number may still change, for all I know they took the number from my post here

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  11. #36
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    Quote Originally Posted by Donwulff View Post
    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.
    Hi Donwulff

    I am the one who has the Verified Purchase on Amazon UK and I am the guilty one who added the review on to Amazon on the 5th September 2017 and I am sorry if my partial review looked like Dante Labs press release. I also bought another WGS for my wife few weeks later (23 September 2017) and my sister bought a WGS few days later after me in Iceland. I think she received and sent her sample back with DHL on the 13 September 2017). The sample for my sister was sent from Rome, Italy with DHL.

    I have been in touch with Dante Labs few times since I bought my sample kit for WGS and they have always been very fast replying to my emails and their answer are exemplary and very detailed.

    I am sure that Dante Labs are for real and I wish them great success but I have a lot hinging on my believe that they are just trying to find their way in a difficult business world.

    However, I did contact Dante Labs this morning (6 November 2017) and I asked when I can expect my WGS test results:

    Here is a copy of my email to Dante Labs:

    "Dear Dante Labs

    The reason why I am writing to you today is to check when the results of my Dante Labs Full DNA Analysis Whole Genome Sequencing (WGS), 30X Coverage will be forwarded on to me.

    I placed my order through Amazon UK. Order #205-5594037-XXXXXXX on the 5 September 2017 and I posted my spit sample on the 6 September 2017 with DHL. This was 8 weeks ago and as I was expecting the results to arrive in 6-8 weeks. The 8 weeks cut-off date makes it today from the date of shipping my sample to Dante Labs in Rome, Italy.
    "

    ...and Dante Labs answered my email with this reply.

    "Our lab is completing the bioinformatics analysis on your sample. You are expected to receive results by the end of November"

    To receive my WGS test results at the end of November is perhaps not ideal but no serious hardship is done, that is if I do get my results by the end of November at the latest.

    I intend to keep you all informed how I get on at the end of November.

    Best regards

    jenssonjoi
    Last edited by jenssonjoi; 11-06-2017 at 05:29 PM. Reason: Correcting typos

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  13. #37
    Quote Originally Posted by Donwulff View Post
    Did you get your results yet? I don't want to be recommending them if their delivery seems dodgy. As said mine was some weeks late too, but nothing drastic, and they shared a post from happy customer on Facebook, but otherwise I've heard little.
    Still no results. This Friday will be 14 weeks. I've been in contact with them again and they said they'd look into my order specifically. It's worth noting that they've changed the estimate on their site to 50 business days (so about 10 weeks).

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  15. #38
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    It is 9th week for the first sample I have sent to them. So, still waiting. We will see next week.

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  17. #39
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    Quote Originally Posted by rbtlsr View Post
    Just wanted to say that I'm still waiting on results. I mailed my kit in on 8/4, so it's been over 12 weeks. When I originally contacted them a few weeks ago they said I'd have it by 10/20, then I contacted them again when that date came around and they're now saying 11/3.

    I asked if I could get the vcf as soon as it was available without having to wait for the report to be developed, and the person I was in contact with looked into it but unfortunately they can't do that, so I have to wait until everything is ready.

    I'm trying not to get too impatient because they're a new company and it was a ridiculously low price, but I'm really looking forward to getting my data.
    RBTISR

    Did you get your results back from Dante Labs?

  18. #40
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    In the beginning of the 10th week I received results of my WES analysis. I have got an email that reports are available for the test.
    I was able to download a VCF, which is aligned to GRCh37 and contains two files - one for SNPs and one for INDELS.
    Right now I am trying to use them with Promethease, and I have uploaded uncompressed VCF for SNPs to GEDmatch.com
    Wellness and longevity report report is very strange. It is some file from sequencing.com, but I see the information as not useful. It is produced by the Genome viewer App at sequencing.com and contains a lot of statistics about reads, aminoacids and so on. I have not seen any 100-pages report about my traits or disease risks and protections. It would be an complete abracadabra for a general average user. I haven't been able to find any direct useful health information there.
    I've contacted the customer service about alignment to GRCh37 and they have answered that FASTQ files are provided for customers and the files could be aligned to any genome reference. That is nice. I have not seen any FASTQ or BAM files for direct download from the page. I will wait with contacting the customer service for the files because I am waiting for my WGS and have more samples from my relatives. I want to see how WGS results are and which reports are provided then.
    If you are planning to test WES for possible disease risks, than you have probably to use some third party service or have a bio/medical-analyst to interpret your test results.
    After the contact with some genealogist I can say that WES is not recommended for genealogical purposes. I write more when I have got my WGS results.

    Well, the current price for WGS and WES is a hard competition compared to other services around or above 1000$, another good point is European market and very fast delivery with DHL. The customer service is friendly and responsive. They still need to improve their reports and FASTQ and BAM files should be available for download directly from the account, at least for a limited time, hm... 30 days after the completion and upon a later request. The Wellness and Longevity report is of an inferior quality so far and should be improved.

    PS Some part referred as Quality in Number of effects:
    Quality:

    Min 30
    Max 20,628
    Mean 2,159.85
    Median 1,092

    If it is about number of reads than it is superior I think.

    The report from Promethease was a lot more informative than Promethease based on the analysis of the data from AncestryDNA.
    Last edited by karwiso; 11-13-2017 at 10:59 PM.

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