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Thread: Dante Labs (WGS)

  1. #1021
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    Quote Originally Posted by Petr View Post
    Before filtering
    total reads: 667.495810 M
    total bases: 99.125328 G
    Q20 bases: 96.030385 G (96.877748%)
    Q30 bases: 90.925155 G (91.727470%)
    GC content: 43.566229%
    After filtering
    total reads: 662.534472 M
    total bases: 98.299320 G
    Q20 bases: 95.480444 G (97.132355%)
    Q30 bases: 90.481013 G (92.046428%)
    GC content: 43.541445%
    Filtering result
    A 30x WGS test should have better than 90gBases. These files easily exceed that amount.

    Now the BAM should be investigated for genomic territory covered. You could use GATK's CollectWgsMetrics. MEAN_COVERAGE should be about 30x. If it's significantly lower, you had a higher bacterial concentration sequenced than normal.

  2. #1022
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    Quote Originally Posted by Petr View Post
    Before filtering
    total reads: 834.317408 M
    total bases: 125.147611 G
    Q20 bases: 121.528261 G (97.107935%)
    Q30 bases: 115.666626 G (92.424158%)
    GC content: 40.918799%
    After filtering
    total reads: 827.816768 M
    total bases: 123.827389 G
    Q20 bases: 120.561766 G (97.362762%)
    Q30 bases: 114.859232 G (92.757534%)
    GC content: 40.873596%
    Much higher than expected. That's closer to 40x coverage and would be atypical.

  3. #1023
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    Quote Originally Posted by teepean47 View Post
    Before filtering
    total reads: 347.074070 M
    total bases: 51.605934 G
    Q20 bases: 49.989405 G (96.867553%)
    Q30 bases: 47.543664 G (92.128290%)
    GC content: 42.797089%
    After filtering
    total reads: 342.757768 M
    total bases: 50.954371 G
    Q20 bases: 49.556123 G (97.255882%)
    Q30 bases: 47.189698 G (92.611679%)
    GC content: 42.717622%
    Helps to confirm what I've seen in the Y-chromosome data added to the Y-DNA Warehouse. These tests are actually 15x+ to date. The real question is why are they overshooting the mark so much? Why not market as 15x if this is expected?

  4. #1024
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    Summary of all my WGS 30x tests from Dante, total bases after filtering and coverage calculated for idxstats:

    2018-01-19: 118 G - 32.8x - 12.4 % of unmapped reads
    2018-03-23: 125 G - 32.7x - 8.3 % of unmapped reads
    2019-03-27: 124 G - 38.7x - 1.8 % of unmapped reads
    2019-03-27: 89 G - 27.5x - 3.3 % of unmapped reads
    2019-03-27: 102 G - 25.5x - 20.7 % of unmapped reads
    2019-03-27: 93 G - 21.0x - 28.5 % of unmapped reads
    2019-06-05: 106 G - 29.4x - 12.8 % of unmapped reads
    2019-11-12: 98 G - mapping not processed yet
    2019-11-14: 73.7 G - mapping not processed yet
    Last edited by Petr; 11-14-2019 at 11:05 PM.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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    Quote Originally Posted by JamesKane View Post
    Helps to confirm what I've seen in the Y-chromosome data added to the Y-DNA Warehouse. These tests are actually 15x+ to date. The real question is why are they overshooting the mark so much? Why not market as 15x if this is expected?
    Weird thing is that YFull refused to accept this. According to their customer service: "Unfortunately, the quality of the sequence is extremely low for the Y chromosome".

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    Quote Originally Posted by teepean47 View Post
    Weird thing is that YFull refused to accept this. According to their customer service: "Unfortunately, the quality of the sequence is extremely low for the Y chromosome".
    Can you ask them for the stats they used to reject it? If its not a trade secret.
    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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  9. #1027
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    Quote Originally Posted by MacUalraig View Post
    Can you ask them for the stats they used to reject it? If its not a trade secret.
    The only answer I got was it is 2x. I did ask again but I doubt I get an answer. Maybe they don't want to anger their new business partner... I honestly thought Dante's 4X would be the perfect cheap test to cover everything.

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  11. #1028
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    The results of WGS 30x received today have somewhat lower average number of reads:

    General
    fastp version: 0.20.0 (https://github.com/OpenGene/fastp)
    sequencing: paired end (151 cycles + 151 cycles)
    mean length before filtering: 148bp, 148bp
    mean length after filtering: 148bp, 148bp
    duplication rate: 5.775481%
    Insert size peak: 261
    Before filtering
    total reads: 502.517378 M
    total bases: 74.698229 G
    Q20 bases: 72.112478 G (96.538403%)
    Q30 bases: 68.185465 G (91.281233%)
    GC content: 41.676315%
    After filtering
    total reads: 497.104320 M
    total bases: 73.690341 G
    Q20 bases: 71.416587 G (96.914448%)
    Q30 bases: 67.614213 G (91.754512%)
    GC content: 41.600758%
    Filtering result
    reads passed filters: 497.104320 M (98.922812%)
    reads with low quality: 5.140478 M (1.022945%)
    reads with too many N: 31.094000 K (0.006188%)
    reads too short: 241.486000 K (0.048055%)
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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  13. #1029
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    Quote Originally Posted by teepean47 View Post
    The only answer I got was it is 2x. I did ask again but I doubt I get an answer. Maybe they don't want to anger their new business partner... I honestly thought Dante's 4X would be the perfect cheap test to cover everything.
    Please could you clarify is your results filtered for Y only or not?

    For example here https://anthrogenica.com/showthread....l=1#post611568 statistics for 4x says: "ChrY... 29.20% Coverage and 1.66 Mean Depth" Could you show your output by BamDeal?

    As Y DNA Warehouse statistics page also says: "On average WGS tests have fifty percent of test's rated depth covered in the Y chromosome e.g. a 15x test has 7 reads spanning each location". 4x -> 2x should be ok.

    I am considering 4x as a great (and very cheap) option to get a brief autosomal DNA + mtDNA + might be some of Y (if it is possible), so it would be nice even if sometime accidentally they are producing better Y results.
    Last edited by mdn; 11-15-2019 at 07:53 AM.

  14. #1030
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    For comparison I once loaded a WGSx4 (FGC low pass) to YFull and have several YSEQ with a Y depth median 7-8x, my worst YSEQ has been 6x (on the Y) and those were all accepted. YFull have a very good relationship with YSEQ of course.

    I didn't bother uploading my WGSx2 though.
    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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