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Thread: Dante Labs (WGS)

  1. #21
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    Cost about $10 to serve the BAM file off Amazon S3 for YFull; since YFull pulled it almost immediately I could've deleted it right away so storage costs just pennies.

    I was going to leave it there in case I get around to running some further analysis on Amazon AWS myself, but then I took a closer look at Sequencing.com who advertise Dante Labs as their sequencing partner, and noticed they offer free storage and transfer for unlimited amount of DNA data at least for now. So if you trust sequencing.com and don't have another reliable cloud drive, you can actually just use their Big Yotta client to upload the BAM file on their site, and serve the link off there. It might even be possible for Dante Labs to put it there, but I didn't ask.

    My BitDefender antivirus did not play nice with Big Yotta though, and I had to add the BAM file to antivirus exclusions; not that there's a virus there, but the way Big Yotta accesses it causes BitDefender to lock up CPU & drives re-scanning all the time.

    Sequencing.com offers a few other cloud-based automated tools that are free; sadly despite claiming to process BAM files their EvE Free pipeline won't let me select my BAM file, so the only free tool that currently works is "Genome VCF" for generating gVCF v4.1 off the bam file, which *might* solve the problem of REF-calls not being listed in the original VCF. Trying out how it goes; though again, hopefully Dante Labs can offer this for most folks in the future.

  2. #22
    Registered Users
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    724
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    Location
    Glasgow, Scotland
    Ethnicity
    Pictland/Deira
    Y-DNA
    R1b-M222-FGC5864
    mtDNA
    H5r*

    Quote Originally Posted by Donwulff View Post
    Cost about $10 to serve the BAM file off Amazon S3 for YFull; since YFull pulled it almost immediately I could've deleted it right away so storage costs just pennies.
    Please post a screenshot of the 'RAW data - Statistics' tab which should be the URL https://www.yfull.com/raw-data-stat/. This should be populated very shortly (a matter of hours) after they receive your file.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content

  3. #23
    Junior Member
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    Oddly enough, Y chromosome stats remains empty save for "ChrY BAM file size: 0.95 Gb" vs 0.41 Gb for BigY, but STR & mtDNA sections were populated almost immediately (though not available yet). 355 (71.00%) Reliable Alleles vs. 422 (84.40%) for Big Y; it makes sense because my Big Y was with 120bp read length, while the Dante Labbs WGS is just 100bp so longer STR's can't be read. This is weird, because the STR results used to lag months behind SNP's. I were them, I'd calibrate the SNP's against my existing Big Y test before using them, so perhaps that's what they are doing. Not batched yet for next processing batch either, just "the samples are collected for a next batch" with last months target time; I'm not sure what YFull is supposed to look for new samples nowadays. It may not get processed until the next batch starts.

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