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Thread: Dante Labs (WGS)

  1. #1101
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    Quote Originally Posted by tontsa View Post
    How would you guys go about combining multiple runs of 5x-30x WGS? I have 100bp BGI one and then 30x and 5x with Illumina 150bp reads. I've had mixed results of creating one BAM and then variant calling that.. not yet sure how to go about comparing variant calling individual BAMs and then merging the vcfs somehow.
    I was thinking about something similar: combine two FASTQ/BAM-files depending on read quality. So use one FASTQ/BAM to improve another.

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    Quote Originally Posted by tontsa View Post
    Atleast I got exactly the same fastqs as was on HDD I received back in April 2019 or so for 2018 Black Friday kit.. the BAM was newly generated with Dragen though but referenced atleast same files. I haven't really looked into that BAM too closely as I don't need hs37d5 aligned one currently.
    Thanks for posting this. Just checked, and the kit I've been posting about now has BAM and FASTQ posted for download. I wish they could keep their story straight. When I ordered it, they said raw data would be downloadable. Then they said no way, gotta pay for the drive. Then I paid for the drive and they sent it about 6 months later. Now a few months after that and it is online. I have not bothered to download them yet to compare to the files on the drive.

  3. #1103
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    Blaine Bettinger has got his raw data and made some long posts about it on his big fb group which has kicked off some interest. He used the YSEQ remapping service.

    He mentioned that he expected having a WGS chapter in the next edition of his book which would be good.
    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. #1104
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    yesterday tested the download from Dante Labs, 36 GB BAM file came down in 27 minutes, so this maxed out my 200 Mbit/sec Internet line, I must say excellent speed. Also the i run fastp on it>
    sequencing: paired end (151 cycles + 151 cycles)
    mean length before filtering: 147bp, 147bp
    mean length after filtering: 147bp, 147bp
    duplication rate: 5.237798%
    Insert size peak: 261
    Before filtering
    total reads: 622.063512 M
    total bases: 91.707459 G
    Q20 bases: 89.236250 G (97.305334%)
    Q30 bases: 85.153134 G (92.853008%)
    GC content: 42.444874%
    After filtering
    total reads: 616.151406 M
    total bases: 90.678039 G
    Q20 bases: 88.540228 G (97.642416%)
    Q30 bases: 84.579331 G (93.274327%)
    GC content: 42.377279%
    Filtering result
    reads passed filters: 616.151406 M (99.049598%)
    reads with low quality: 5.595058 M (0.899435%)
    reads with too many N: 13.404000 K (0.002155%)
    reads too short: 303.644000 K (0.048812%)

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  7. #1105
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    Quote Originally Posted by Petr View Post
    The coverage counted using idxstats form the original hg19 bam files supplied by Dante, and hg38 bam files created by myself using the procedure described by James Kane:

    Kit 1: (98.3 Gbases): coverage 15.57x, 51.23 % unmapped - hg38 JKane: coverage 16,55x, 47.19 % unmapped
    Kit 2: (73.7 Gbases): coverage 22.21x, 7.69 % unmapped - hg38 JKane: coverage 22.30x, 6.35 % unmapped
    Kit 3: (97.8 Gbases): coverage 30.78x, 3.34 % unmapped - hg38 JKane: (not processed yet)

    What could be the reason for so many unmapped reads for Kit 1? High contamination of the original sample? Or the 8 months storage of the sample by Dante?
    Quote Originally Posted by Donwulff View Post
    Too many possibilities to answer. In principle, I believe DNA GenoTek https://blog.dnagenotek.com/ for example seems to promise years of storage at room temperature. However, this is assuming the stabilizing buffer is added promptly. In addition, your sample was probably also collected on SPECTRUM, while I recall Dante Labs saying they switched kits specifically because the new one provides higher quality, I've not seen any specs or studies supporting that.

    Seeing read-quality of the unmapped reads (I can't, unfortunately, recall if any QC software readily provides that) to see if it's degraded DNA or results of mapping against some microbial references (I have oral on the "Dante Labs technical" thread, but I'm thinking one of the high-level classifiers could be useful too for mold etc. I have to say that 15.57X is certainly concerning for something sold as 30X. The microarray genotypes also seem to have individuals who never have enough DNA in the sample though, so I'm sure there's outliers and mis-applied stabilizing buffer etc.
    I've had two kits done with a similar mapping/ QC issue on my Kit1.
    Kit1. Purchased Feb2019, returned by a slow mail (even though paid for tracking etc as I mistakenly ordered from the US site and they only send a return address if I post from the Us. I did contact them and was not offered any help. This kit was delayed in US customs, and presumably Asian customs, then US customs again and then Italian customs. So months when it was not in ideal conditions. That said they insist it can be out in the heat of 50C or minus (as it was during the big freeze in the US last winter). My usual wait in US customs with parcels and mail is 5 weeks, I've had up to 9 weeks for a saliva sample to clear customs.
    this is my husband's kt. We were careful in taking the saliva. I wore gloves, a plastic apron, clean washed hard floor environment. taken first thing in morning with no drink, food since evening before. Cleaned teeth and mouth well night before. etc. My husband does have PhD in biology if that adds to the point that it was NOT the collection process. (although the kit sample now reads you can clean teeth one hour before), that was not how the advice used to read a couple of years ago when I took FTDNA, ancestry etc samples. Stabilizing buffer applied immediately. Stored in cool place at room temp until posted that day, and stored in cool place at PO until collected by mail truck on a coolish day (all considered in collection). Time was also after the extremes of temperatures had passed for transit. Parcel tracking paid and left Australia promptly. Kit2 received by Dantein Utah in March 2019 I think, maybe April-I'd need to check that.

    Kit2. Purchased directly from EU site and collected by DHL, and returned to Italy and finished processing and reports very fast. Collected Fri
    22 Nov 2019 in Australia, finished processing and report loaded by 3Dec 2019 in Italy. I didn't notice until I got home on 13th Dec. Everything there. DHL expedites thru customs. This kit was also collected with care and consideration to temperature and picked up promptly by the DHL courier.

    Kit1: using FASTQ1 49.99Gbases, FASTQ2 49.97 Gbases(using FQSUM). But running bam.iobio I get 61.7 % mapped reads, with 83.4% proper pairs, 6.1%singletons, 87.8% both mates mapped, 8.5% duplicates
    https://www.facebook.com/groups/5589...0295888387034/
    gives almost a 20X, but I am unsure whether it is so corrupted it can be trusted that much?

    kit2: is set to the new minimum no of reads of 90GB(using FQSUM) it seems but gave me almost a 30X.
    90.4% mapped reads, 98.1% proper pairs, 0.6% singletons, 98.6% both mates mapped, 7.1% duplicates

    I was assured it was NOt the delay or sitting around in customs or transit that may have caused degradation of the sample. Both kits had stabilizer applied immediately, both taken with utmost care and stored until sent with care. (room temp -aircon set to 20C). I read the tech stuff about the kits and stabilizer and even emailed them. I am assured it can withstand 50C on the tests they provide, for months. I am unsure if I agree with this though. If not, how does the sample get so contaminated... Ok, it could be viruses? he does have a lurking shingles virus , but at time of collection was healthy enough to not show any symptoms. Otherwise, with at least two of us with similar issues,.. maybe it is some problem with dante labs. I do wonder what Dante's QC test is and how these kits passed it?
    Last edited by Jan_Noack; 12-16-2019 at 08:34 AM.

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  9. #1106
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    I had mixed results with FASTQ files from Dante Labs since they started their in-house lab.
    Four out of six kits were small, two were only 6.7M bases, 2.1X coverage.
    Thanks to the members of the Dante Labs Customers FB, I tried redownloading the FASTQ files from the Dante Labs site.
    3 of the 4 small kits are now significantly larger. You can check to see if the files are bigger by starting the download and then cancelling if the file size isn't larger. I've been checking my fourth small kit that way to see if eventually it is replaced as well. Good luck!

    Old/New FASTQ total reads using fastp
    Old New
    6.7 137.4
    6.6 84.3
    55.4 107.5
    YFull: YF14620 (Dante Labs 2018)

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    Quote Originally Posted by Mansman View Post
    Is dantes lab any good?
    During sales it is 5-10 times cheaper than any competitor (sale = 30x WGS price is 169€).
    But for 99.9% potential users the provided output is clearly not enough. Either you will need to spend a lot of time to understand what you can do 'for free', or you will need to pay more to some other company.

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    (regarding to upgrade from Intro)
    Quote Originally Posted by teepean47 View Post
    I ordered it and I assume (hope) they know what they are doing I only have one kit so it shouldn't be too difficult.
    Have you received any update?
    My 4x ready for 'upgrade' is still not touched - but seems I will need to write to the support.

  12. #1109
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    My 4x upgrade hasn't moved.. nor has resequencing of one 30x kit.. they are prolly again swamped from all the sale campaigns that we have to wait months or year for something to happen..

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  14. #1110
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    Quote Originally Posted by tontsa View Post
    How would you guys go about combining multiple runs of 5x-30x WGS? I have 100bp BGI one and then 30x and 5x with Illumina 150bp reads. I've had mixed results of creating one BAM and then variant calling that.. not yet sure how to go about comparing variant calling individual BAMs and then merging the vcfs somehow.
    I'm currently struggling with this issue. I have 3 BGI kits and 7 Illumina kits with repeated individuals within both BGI and Illumina and across the two. When I tried to use bcftools mpileup with bams from BGI and Illumina together, mpileup ignores the Ilumina kits. But when I run mpileup separately on BGI and Ilumina kits it seems to work reasonably. I've tried every option I could find for mpileup without success in handling both BGI and Illumina together.

    I was motivated to work with the bam files Dante Labs provided because they had fairly reasonable coverage. Their Illumina FASTQs however were sometimes very small, <7G bases read in two cases and only 2/6 were close to 90G bases.

    In the meantime it's been brought to my attention (on the Dante Labs customer FB group) that in some cases the FASTQs on Dante's site have changed. 3 out of 4 of my kits that were small are now 85G or even bigger. So now I'm contemplating realigning the FASTQs.

    But just out of curiosity, has successfully combined BGI and Illumina bams using bcftools mpileup (or any other method)?
    YFull: YF14620 (Dante Labs 2018)

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