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Thread: YSEQ's new 15x WGS

  1. #31
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    At one stage they were offering a GEDMatch ready upload file so maybe ask them about that.

    You could spend the rest of your life analysing a WGS file, depends on what you are interested in.
    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, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  3. #32
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    One thing I noticed when I put my Yseq WGS autosomal results file through Promethease is that only snps that I was positive for and novel variants were included in the results, snps that I am ancestral for didn’t seem to be included . Or at least thats what I inferred from the fact Promethease couldn’t predict my blood type unless I used the Yseq 23andme format file because there was no result on the main autosomal results file for some of the snps used to predict it (they were included on the Yseq 23andme format file) .I suppose its a way to reduce the file size. Or perhaps something went wrong with Promethease.
    Any one else notice this or is it just me?

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  5. #33
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    There are 3 billion base locations included in your WGS test results. By default callers only look for locations where you do not match the reference genome, since the variant call file would be larger than your BAM if all sites were included. YSEQ will create a file that's in the same format as 23andMe that can be uploaded to Gedmatch, if you'd want. Only about 500-900 thousand call sites are included in that report.

    For the most part they only offer analysis on the Y and mitochondrial portions of their WGS tests. This is delivered as a summary of where you fit and recommendations of any additional testing that might be useful to clear up questionable results.
    Last edited by JamesKane; 01-17-2019 at 11:22 AM.

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  7. #34
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    Quote Originally Posted by MacUalraig View Post
    At one stage they were offering a GEDMatch ready upload file so maybe ask them about that.
    I did, and I got a response very quickly from them. YSEQ always has courteous and prompt service, and in this one respect their service is quite satisfactory. They're allowing YFull access to my results, too.

    So, since comparing results is so much fun with DNA tests, here's my Genesis GEDmatch from my YSEQ test:

    Population

    North_Atlantic: 45.16 Pct
    Baltic: 26.98 Pct
    West_Med: 13.36 Pct
    West_Asian: 3.43 Pct
    East_Med: 7.28 Pct
    Red_Sea: 0.85 Pct
    South_Asian: 1.25 Pct
    East_Asian: -
    Siberian: 0.86 Pct
    Amerindian: 0.47 Pct
    Oceanian: -
    Northeast_African: 0.20 Pct
    Sub-Saharan: 0.16 Pct

    My pre-Genesis GEDmatch results from my FTDNA test, which remained static except for a reduction of my SSA from 0.16 to 0.15. Have to double-check to see if there's any other changes, but this is what it says now:

    Population

    North_Atlantic: 44.08 Pct
    Baltic: 27.57 Pct
    West_Med:13.67 Pct
    West_Asian: 3.04 Pct
    East_Med: 8.05 Pct
    Red_Sea: 0.70 Pct
    South_Asian: 1.39 Pct
    East_Asian: -
    Siberian: 0.91 Pct
    Amerindian: 0.33 Pct
    Oceanian: -
    Northeast_African: 0.10 Pct
    Sub-Saharan: 0.15 Pct

    I'm waiting for my new YFull/YSEQ results, that might be a few days, but I uploaded to DNA.Land and really got a difference. Matter of fact, I should post that in the DNA.Land forum. Anyhow, this was really nice. Affordable WGS, a sign of a happy future.
    "Bid me discourse, I will enchant thine ear..."

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  9. #35
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    I got my own WGSx30 back overnight, my sample got back to the lab on Dec 14th. The Y BAM is downloadable at 343Mb but the full BAM is 32Gb so I will be awaiting the postal version of that. Brief skim through the reports indicates they didn't find any new good quality Y SNPs that I didn't have already from my Y Elite 1.0 but I'm uploading it to YFull for a second opinion.
    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, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  11. #36
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    Adding a set of histograms for YSEQ's WGS products as pertains to the Y chromosome. I may publish a link to a blog post that does all contigs with my 30x sample, but don't hold your breath.

    15x WGS: (Note: Two of these really seem to be 20x)


    30x WGS:


    50x WGS:

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  13. #37
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    Got my disc with my full WGS bam yesterday so plenty to play around with now.

    As regards coverage it seems to vary quite a bit and one x15 kit seems to have got as good depth as my x30 on the Y.
    Mine: mean 14.67x median 14x (roughly the expected value for a WGSx30)
    x15: mean 14.14x median 14x

    Range seem to date on x15: mean 6.31-20.68x, median 4x-18x
    DNA volume: 14 to 215 microL
    Last edited by MacUalraig; 02-26-2019 at 09:32 AM.
    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, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  15. #38
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    A very short blog post containing coverage histograms for the 30x WGS option on all chromosomes is now up. A Bit About WGS Testing

    While the sample is sourced from YSEQ any test with 150 base pair reads running on Illumina equipment will look about the same.

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  17. #39
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    Has anyone other than me tried doing a compare betweeen a real 23andMe report and YSEQ's mocked up 23andMe style report? I started with this as it seemed like a more manageable dataset but was surprised to be honest how many differences there are. Going through the whole thing could be quite a big task.

    In one instance I found the YSEQ "23" call was contradicted not just be 23andMe and my new Dante VCF but the YSEQ BAM file! However despite looking good in IGV it is *missing* from the YSEQ VCF so presumably wasn't called and the 23 script then just wrote it up as ancestral AA instead of AG.
    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, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  19. #40
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    Are you looking at the hg38 BAM? The 23andMe-mock report is done with an hg19/hg37 reference.

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