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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.

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  3. #22
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    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)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  5. #23
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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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  7. #24
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    Hi! Anyone had results back from DANTE? Can you share the experience?

  8. #25
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    Funny, the site won't let me reply to a PM...
    Yes, I did receive my results, though a several weeks late. I can't vouch that everybody will receive them; their pricing remains suspect as ever. The results I got check out in every way, it's the real thing, and YFull is currently analyzing them for Y chromosome & mtDNA.

    There's some challenge with their formats so far, because they provide only VCF file of sites that differ from the reference build, and with an outdated mtDNA sequence. In my case, they also only delivered the BAM file on an USB stick, which while fast, doesn't make it easy to run third party analysis as you will first need to upload it to a 100GB+ cloud storage provider.

    GEDMatch Genesis (Their new beta matching) and SNPedia/Promethease accept their VCF-file link directly, and Sequencing.com can be used besides for storing and serving the BAM file, also to run various kinds of analysis on it, many for free. In that case you may have to add "&.vcf.gz" at the end of the file URL's to get things like GedMatch to realize they're vcf files. This will let you get Genomic VCF and mtDNA alignment from the BAM file and ClinVar annotation (or test mapping to GRCh38 reference) if you can get the BAM uploaded there.

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  10. #26
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    YFull has updated the expected completion date on my Dante Labs WGS sample to 20th November so I guess I'll be able to report on any impressions about theremain, as of yet there's no Y chromosome statistics save for "ChrY BAM file size: 0.95 Gb". From my memory of the Big Y processing, the statistics took a while to fill in as well, and the predicted completion date kept sliding forwards and backwards. I'll probably get around to doing some analysis of my own before then, but I think what YFull gets out of it with their pipeline & quality control is what matters most, so that'll be about a month.

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  12. #27
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    Quote Originally Posted by Donwulff View Post
    YFull has updated the expected completion date on my Dante Labs WGS sample to 20th November so I guess I'll be able to report on any impressions about theremain, as of yet there's no Y chromosome statistics save for "ChrY BAM file size: 0.95 Gb". From my memory of the Big Y processing, the statistics took a while to fill in as well, and the predicted completion date kept sliding forwards and backwards. I'll probably get around to doing some analysis of my own before then, but I think what YFull gets out of it with their pipeline & quality control is what matters most, so that'll be about a month.
    My memory may have been at fault. I admin a group on YFull but you can only join groups when the SNP analysis is complete (and hence the statistics tab populated).

    In the meantime you could do some simple examination of the data locally eg compare read depths and calls at your previously determined NVs.
    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) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  14. #28
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    It's been a few years since I got my BigY done, and this is a new situation since my sample may be first one from Dante Labs they have so it may be handled differently.
    I'm not sure I should post my novel SNP's publicly, but what the heck, that's probably the most significant part. Out of the VCF provided by Dante Labs, most of my novel SNP's aren't listed. The sequence is nominally 30X, however the Y chromosome is haploid, ie. there is only one copy, which means you could expect average read depth of about 15 reads, and if Dante Labs filters for example expect at least 12 reads to report it, then most SNP's won't end up on the VCF. BigY is by design much deeper sequence, and the variants matching Dante Labs have from 24 to 85 reads on YFull, typically 50 to 80 as per the BigY spec.

    The main benefit from WGS is you're supposed to get areas outside of the targeted locations of Y-chromosome, so novel SNP's not found on BigY are highest interest but will require YFull to finish their analysis. Comparing to the novel SNP's found on BigY by YFull will give some idea of utility as the only test. In conclusion all of the Acceptable and Good Quality SNP's can be called on Dante Labs sequence, though only about two thirds pass filters on the VCF they provide. Read-depth at my current terminal Y-SNP is 25; the terminal/haplogroup detemining SNP's are usually ones which are easy to determine by sequencing, because they need to match in all samples.

    I have 6 Best Quality novel variants on YFull off the 150bp PE Big Y, and Dante Labs VCF includes these 4 out of them and Sequencing.com Genome VCF finds them all (italics):
    chrY 9427939 . T C 747 PASS DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLE AC=2;MLEAF=1.00;MQ=46;MQ0=1;QD=35.57;SB=-2.700e+02 GT:AD:DP:GQ:PL:MQ:GQX 1/1:1,20:21:60:780,60,0:46:60
    chrY 16307293 . G A 460.77 PASS AC=2;AF=1.00;AN=2;DP=20;FS=0.000;GQ_MEAN=60.00;MLE AC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=23.04;SOR= 0.892;VQSLOD=1.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,20:20:60:489,60,0
    chrY 17173949 . C T 509.77 PASS AC=2;AF=1.00;AN=2;DP=22;FS=0.000;GQ_MEAN=63.00;MLE AC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=24.27;SOR= 1.828;VQSLOD=1.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,21:21:63:538,63,0
    chrY 19070707 . T C 293.77 PASS AC=2;AF=1.00;AN=2;DP=19;FS=0.000;GQ_MEAN=52.00;MLE AC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=15.46;SOR= 0.793;VQSLOD=2.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,19:19:52:322,52,0
    chrY 20063414 . G C 366 PASS DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLE AC=2;MLEAF=1.00;MQ=53;MQ0=0;QD=33.27;SB=-1.987e+02 GT:AD:DP:GQ:PL:MQ:GQX 1/1:0,11:11:30:399,30,0:53:30
    chrY 20063416 . G C 467.77 PASS AC=2;AF=1.00;AN=2;DP=12;FS=0.000;GQ_MEAN=36.00;MLE AC=2;MLEAF=1.00;MQ=54.16;MQ0=0;NCC=0;QD=27.40;SOR= 1.022;VQSLOD=1.72;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,12:12:36:1|1:20063414_G_C:496,36,0

    17,5 average read depth. NB. Sequencing.com Genomic VCF has 1 read read less for some locations.


    Out of my 8 Acceptable Quality SNP's on YFull, Dante Labs has reported 5, and Sequencing.com Genomic VCF has the rest:
    chrY 8341974 . G T 606 PASS DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLE AC=2;MLEAF=1.00;MQ=60;MQ0=0;QD=33.67;SB=-3.160e+02 GT:AD:DP:GQ:PL:MQ:GQX 1/1:0,18:18:51:639,51,0:60:51
    chrY 8420303 . G T 464 PASS DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLE AC=2;MLEAF=1.00;MQ=60;MQ0=0;QD=35.69;SB=-2.349e+02 GT:AD:DP:GQ:PL:MQ:GQX 1/1:0,13:13:39:497,39,0:60:39
    chrY 9167511 . C T 457.77 PASS AC=2;AF=1.00;AN=2;DP=19;FS=0.000;GQ_MEAN=57.00;MLE AC=2;MLEAF=1.00;MQ=58.41;MQ0=0;NCC=0;QD=24.09;SOR= 1.609;VQSLOD=1.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,19:19:57:486,57,0
    chrY 15349787 . G C 484.77 PASS AC=2;AF=1.00;AN=2;DP=20;FS=0.000;GQ_MEAN=60.00;MLE AC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=24.24;SOR= 0.892;VQSLOD=1.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,20:20:60:513,60,0
    chrY 17172702 . G T 524.77 PASS AC=2;AF=1.00;AN=2;DP=21;FS=0.000;GQ_MEAN=63.00;MLE AC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=24.99;SOR= 0.784;VQSLOD=1.65;culprit=FS GT:AD:DP:GQ:PL 1/1:0,21:21:63:553,63,0
    chrY 17465570 . G A 518.77 PASS AC=2;AF=1.00;AN=2;DP=22;FS=0.000;GQ_MEAN=66.00;MLE AC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=23.58;SOR= 1.085;VQSLOD=2.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,22:22:66:547,66,0
    chrY 18872443 . C G 410 PASS DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLE AC=2;MLEAF=1.00;MQ=60;MQ0=0;QD=34.17;SB=-7.900e+01 GT:AD:DP:GQ:PL:MQ:GQX 1/1:0,12:12:33:443,33,0:60:33
    chrY 22138713 . C A 416.77 PASS AC=2;AF=1.00;AN=2;DP=18;FS=0.000;GQ_MEAN=54.00;MLE AC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=23.15;SOR= 0.914;VQSLOD=1.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,18:18:54:445,54,0

    This comes to average read depth of 17,875.

    Ambiguous and Low Quality SNP's on YFull weren't found on Dante Labs VCF at all, which isn't too surprising since most of them are likely errors or just hard to sequence spots, and Dante Labs VCF doesn't list REF calls. Sequencing.com produced Genomic VCF calls Ambiquous Quality (2 reads on BigY) ones to REF and the one Low Quality (8 reads with one DEL on BigY) to ALT:
    chrY 3393577 . T . . PASS END=3393621;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:18:48:52
    chrY 4319552 . G . . PASS END=4319597;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:28:57:26
    chrY 5650724 . A . . PASS END=5650758;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:23:60:41
    chrY 6403302 . G . . PASS END=6403312;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:20:48:50
    chrY 8066241 . A . . PASS END=8066300;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:18:48:60
    chrY 15444167 . A . . PASS END=15444217;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:15:45:60
    chrY 16395059 . G . . PASS END=16395152;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:19:54:60
    chrY 18702993 . T . . PASS END=18703017;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:13:39:60
    chrY 18819125 . A . . PASS END=18819177;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:16:45:60

    chrY 16742953 . A T 538 PASS DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLE AC=2;MLEAF=1.00;MQ=60;MQ0=0;QD=31.65;SB=-2.220e+02 GT:AD:DP:GQ:PL:MQ:GQX 1/1:0,17:17:45:571,45,0:60:45
    Last edited by Donwulff; 10-21-2017 at 03:53 PM.

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  16. #29
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    YFull's statistics for my Dante Labs sequence filled out today. Dante Labs is on LEFT, BigY on RIGHT. Please note that one-to-one comparison isn't really possible, because Dante Labs is whole genome-wide "shotgun" (named after the random spread) sequence, and BigY is targeted capture deep sequencing test that targets certain well sequencing and phylogenetically informative regions of the human genome build 37. And most notably, sequencing results vary from run to run and sample to sample. Given that, though, the Dante Labs statistics look better than I expected.

    YFullDanteBigYCmp.png

    On their Facebook page Dante Labs shared post of someone else that got their BAM file on an USB stick, which indicates not only are they still using USB delivery, but *he got a better USB stick than me*. Pfft! According to Facebook's translate he seemed pretty happy with the deal & security, though IMO it's still a terrible way of delivery. At least here the courier service will hand out the package to anyone who looks like they might want it, and then it'll be your home computer and network (Or school, library etc. if that's where you use it!) whose security matters, while the VCF file is still sitting on the Internet containing all the relevant data in much more easily digestible form. Of course any enemies powerful enough to use my DNA can already get it from a glass at restaurant or my garbage, so I'm not personally worried, just saying people need to ask Dante Labs to arrange for online link for the BAM files.

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  18. #30
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    My broadband is capped and there is no way on earth I would be going near an online 100Gb BAM file. That's about what I streamed watching the London Olympics and my broadband bill was horrendous. So regardless of how I were to enable YFull to get to it, I would have to have hard copy locally for my own analysis. My own Y Elite BAM was 8.5Gb and I wouldn't want to go much bigger than that for downloading.
    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) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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