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Thread: Dante Labs (WGS)

  1. #1321
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    Quote Originally Posted by aaronbee2010 View Post
    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:



    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.

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  3. #1322
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    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/c...to_dante_labs/

    I'd be more specific if I knew.
    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
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    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  5. #1323
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    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.
    The clock indicates the momentóbut what does eternity indicate?

  6. #1324
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    Quote Originally Posted by hartaisarlag View Post
    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.
    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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  8. #1325
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    Dante in the news in the UK a lot at the moment mostly bad and today I read this in their official support group:

    Dante Labs
    Admin
    This group is no longer active

    and at the top:

    This group is paused
    An admin paused this group on 21 October 2021.

    I'm not a FB expert but it appears that the 'Resume' button below that message is enabled for me, if I click it I get a Confirm button also appearing enabled (I haven't clicked it)

    Resume group activity?
    All admins, moderators and members will be able to create posts, like, comment and more.

    I would have assumed fb would only enable it for admins/mods...
    Last edited by MacUalraig; 10-22-2021 at 04:51 PM.
    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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  10. #1326
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    Quote Originally Posted by hartaisarlag View Post
    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.
    Dante’s VCFs are heavily filtered and by default on GRCh37. First verify you are looking in the correct locations. Then you just may need the BAM.

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  12. #1327
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    James, I agree with you in that using the BAM file would probably be best thing to look at.

    However, hartaisarlag may have a real issue. Many of the Y-SNPs expected for one of my project members seem to be missing from his Dante WGS test results. Some sections of his BAM file show data for about 100bp or so, then a gap with no data, then another section with data, then a gap, etc. This seems to be related to only his Y Chromosome data. I tried aligning his Dante FASTQ data myself and got essentially the same result. This may mean some problem with Dante's actual sequencing operation, but I have no clue what it might be!
    Last edited by dcissell; 11-25-2021 at 04:20 PM.

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  14. #1328
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    Quote Originally Posted by dcissell View Post
    James, I agree with you in that using the BAM file would probably be best thing to look at.

    However, hartaisarlag may have a real issue. Many of the Y-SNPs expected for one of my project members seem to be missing from his Dante WGS test results. Some sections of his BAM file show data for about 100bp or so, then a gap with no data, then another section with data, then a gap, etc. This seems to be related to only his Y Chromosome data. I tried aligning his Dante FASTQ data myself and got essentially the same result. This may mean some problem with Dante's actual sequencing operation, but I have no clue what it might be!
    For Y-DNA data I can take a look on a limited basis, if folks upload the BAMs to ydna-warehouse.org but the exact scripts I use are also available on GitHub as Gists should you prefer to keep the data private.

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