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Thread: Dante Labs (WGS)

  1. #981
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    Quote Originally Posted by teepean47 View Post
    I filtered MT from the VCF and added the original header. Haplogrep gave the result H10g which is correct.
    Thank you, it says H1e. I just do not know the 'proper' haplogroup as the data is for my wife.
    Ok might be I will wait for BAM or FASTQ and will check with another instruments.

  2. #982
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    So some statistics on Intro 4x.

    Monday noon - initial result with VCF (SNP и Indel).
    Tuesday evening additional 2 VCF (CNV + something else).
    Wednesday evening - FASTQ R1 и R2 (20 gb each)
    Thursday evening - BAM (20 gb)

    BamDeal stats (it is a girl, so some strange Y with 0.64% coverage and 0.05 mean depth is removed):
    #ID Length CoveredBase TotalDepth Coverage% MeanDepth
    1 249250621 221955859 2241274580 89.05 8.99
    2 243199373 236104856 2291519659 97.08 9.42
    3 198022430 194221826 1859468480 98.08 9.39
    4 191154276 186638374 1728301243 97.64 9.04
    5 180915260 175745684 1673761356 97.14 9.25
    6 171115067 166756582 1597156474 97.45 9.33
    7 159138663 153434835 1487997908 96.42 9.35
    8 146364022 141330764 1369367867 96.56 9.36
    9 141213431 114186762 1119817234 80.86 7.93
    10 135534747 129253716 1290690007 95.37 9.52
    11 135006516 130412836 1307149460 96.60 9.68
    12 133851895 129858562 1268523973 97.02 9.48
    13 115169878 95300694 888581322 82.75 7.72
    14 107349540 87843774 860996242 81.83 8.02
    15 102531392 79996070 809312638 78.02 7.89
    16 90354753 77335729 873209365 85.59 9.66
    17 81195210 77010661 831590323 94.85 10.24
    18 78077248 74460303 718042436 95.37 9.20
    19 59128983 55306480 621690764 93.54 10.51
    20 63025520 59238733 628993885 93.99 9.98
    21 48129895 34644781 353564696 71.98 7.35
    22 51304566 34098755 387299468 66.46 7.55
    X 155270560 148155109 1396235891 95.42 8.99
    MT 16569 16569 3921325 100.00 236.67

    mtDNA Server stats for MT BAM done by WGS Extractor.
    ===
    Statistics:
    Overall Reads: 176,455
    Filtered Reads: 153,004
    Passed Reads: 23,451
    Passed FWD Reads: 1,690,116
    Passed REV Reads: 1,687,354

    Mapping Quality OK: 25,864
    Mapping Quality BAD: 1,101
    Unmapped Reads: 0
    Wrong Reference in BAM: 149,490

    Base Read Quality OK: 3,377,470
    Base Read Quality BAD: 113,647

    Bad Alignment: 15
    Duplicates: 2,398
    Short Reads (<25 bp): 0
    ===

  3. #983
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    That's big for 4X, definitely strong contender against DNA microarrays if they can keep the quantity (and quality) up. Especially if it could be combined with imputation. Actually I think we can already do that fairly well, drop variant calls below certain quality, run it through imputation and then set discrepant imputed variants as no call. (There's PROBABLY an imputation algorithm that can take variant quality into account and do error-correction on the fly, but I haven't seen those in common use)

    Bit unclear on the read length etc. from those stats though, (3,377,470+113,647)+(25,864+1,101) gives me 129.5 bp, which might mean 160bp reads with 30 bp overlap and/or trim. I have no idea how the mtDNA stats say "overall reads 176,455" and "passed fwd reads" 1,690,116 though. Is the overall reads for whole genome, and passed FWD/REV reads actually bases? Passed reads is probably read templates on chrM, and mapping quality is over alternative mappings as well with "wrong reference" being non-chrM reads including alt-mappings. There's no stat for bases in primary mappings only though which prevents calculating real read length.

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  5. #984
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    Quote Originally Posted by Donwulff View Post
    I have no idea how the mtDNA stats say "overall reads 176,455"
    Sorry WGS Extract produced BAM "chrY and chrM", so there is some trash unknown for me (with coverage of Y 0.64% and 0.05 mean depth). Might be this is a reason.

  6. #985
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    I created an autosomal kit from Dante 4X with WGSExtract and compared it to my Ancestry and FTDNA kits. The results were quite encouraging if one wants to create autosomal kits: Ancestry vs Dante 4X has around 1600 different SNPs out of 900000. With FTDNA the diffrence is around 300 out of 680000.

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  8. #986
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    Studies like https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370902/ have shown empirically that concerdance drops sharply below about ~10X read depth (Average!). 8X-9X is right near the sweet spot, if it actually were the 4X that's promised, it would be really poor even for the sites with coverage. Consequently, the concordance depends heavily on the exact read depth they hit, so YMMV, literally.

    In fact though, your figures seem like they might be slightly higher concordance than in the study (especially since in the study they filtered suspicious calls from the microarray). One caution is in the study they used fixed confidence level for the sequence, and didn't really test the effect of different confidence levels. I suspect that using the new GATK Best Practices recommended convolutional neural network filter and higher required confidence the concordance could be pushed even higher. Perhaps I should try sub-sampling down a sequence and testing it out.

    Of course, the majority of the error is driven by heterozygous variants, where all the sequenced reads happen to hit copy from the same parent (same chromosome from a pair) which will statistically happen a lot over a large genome like the human genome, and is hard to detect. The probability for second read to hit same copy is 50%, three it's 25%, you need 8 reads to push it below 1% (0.78%) out of variants that look homozygous. That filter would give you almost 50% of no-calls though. This is also main reason why rare variants will have more errors, because they're almost always heterozygous.

    In general, you should be able to trust variants which appear heterozygous (ie. one copy out of two) in the sequence, but there's a chance of missing some variants entirely, or reading them as homozygous when in fact heterozygous. Filtering variants called as homozygous at read-depth below 14 should have very high concordance according to that paper. A lot of clinical reports though just say "variant exists" which is playing it safe, without specifying whether it's hetero or homozygous, or that there isn't a variant. VCF files need an extension that says the same...

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  10. #987
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    Dante to sequence 100k Mediterraneans!?

    "“We will sequence the genomes of 100,000 people from Africa, the Middle East, and Europe in the next 3 years”, says Dante Labs CEO Andrea Riposati."

    "Early partners will be announced in the next few weeks. Universities, hospitals, research centres and biobanks are invited to apply at the Ulysses Genome Project website."

    https://www.dantelabs.com/blogs/news...genome-project

    Can't find such a genome project website so far mind.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
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    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

  11. #988
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    Even better TODAY there is a Dante webinar at which they will reveal amongst other things...

    drumroll...

    "the truth behind the delays"!!

    https://www.dantelabs.com/pages/webi...ide-dante-labs
    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)
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  12. #989
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    Might be new queues since tomorrow - announced big discounts by YFull and MyTrueAncestry (for DanteLabs).
    Some quote from YFull announce:
    "Dear friends, a couple of news for the community.

    1) Transfer the BAM file from Dante Labs to YFull will be more convenient and easier

    Dante Labs company plans in December 2019 for all its customers (for those who have received their results earlier and for future users) to add the ability to request for free charge the generation of a BAM file (in a special widget on the website), which will include only Y and/or MT Chromosomes. The user will be able to download this BAM file (Y+MT) to your computer or send a direct link in the order form on the YFull website. This option is preferable. We hope that after this the transfer of the BAM file for analysis will be simple and accessible to everyone!

    2) Special extra discount for YFull users from Dante Labs dedicated to "China's Singles Day"

    You can make a discounted order from 11pm CET (Europe) or 5pm eastern time (USA) on Sunday, November 10, 2019 on until Monday, November 11, 2019.

    The price for the WGS (Whole Genome Sequencing) 30X on the Illumina NovaSeq 6000 will be $199.

    For YFull users with the "YFULL10" code extra 10% discount, and the price for the WGS (Whole Genome Sequencing) 30X on Illumina NovaSeq 6000 will be only $180!

    Discount Code: YFULL10

    https://www.dantelabs.com/products/whole-genome-sequencing"

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  14. #990
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    The YFull linkup is way overdue, we've been asking for it since day one. If they actually deliver the BAMs and the link this could be a game changer. But I've said that before and was wrong...
    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)
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    Hidden Content
    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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