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Thread: YFull vs. FGC

  1. #1
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    YFull vs. FGC

    Has anyone had a BigY BAM file analyzed by both YFull and Full Genomes Corp.? If so, did you find significant differences in the results? Was there value in having both companies do the analysis?

    Thanks,

    Jim

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    Yes, I have done that myself with three BAM files, and I was given the dual results in one more case.

    - FGC gives only a downloadable bundle of text files, whereas YFull offers an online account with a friendly interactive interface (although major results can also be downloaded as CSV files).

    - FGC does not, as far as I know, automatically update comparative results when new genetic neighbors arrive. (I think you can specifically ask FGC to re-run comparisons.) YFull continually updates its comparative results (e.g., shared SNPs vs. unshared SNPs) as new BAM files are analyzed.

    - YFull presents a public current haplotree, with estimated TMRCAs, that is updated at least once a month. FGC does not.

    - YFull offers access to the raw data directly. So for example, if someone asks for the precise results of YF03788 at position 19736631 (ZZ12_1), I can simply copy&paste this:
    Code:
    Sample:	#YF03788 (R-P312)	
    ChrY position:	19736631 (+strand)	
    Reads:	164	
    Position data:	97T 67C	
    Weight for T:	0.581543624161	
    Weight for C:	0.418456375839	
    Probability of error:	0.115320099214 (0<->1)	
    Sample allele:	Y (C or T)	
    Reference (hg19) allele:	T
    The primary reason for submitting a BAM file to both companies would be to update both databases, to maximize the visibility of a particular case (e.g., a member of a rare subclade). So for example, I did this for a member of N-Y7310.
    Last edited by lgmayka; 07-13-2015 at 08:43 PM.

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  5. #3
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    Thanks very much. I have six kits of interest and have YFull analysis for all of them. I was wondering whether FGC would add any value. Looks like not.

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    Quote Originally Posted by jbarry6899 View Post
    Has anyone had a BigY BAM file analyzed by both YFull and Full Genomes Corp.? If so, did you find significant differences in the results? Was there value in having both companies do the analysis?

    Thanks,

    Jim
    Yes I did both and think there is value in doing both. I concur with lgmayka's statements above.

    Yfull ranked 13 novel SNPs as "Best", 10 novel SNPs as "acceptable"
    FGC ranked 19 at 99%, 5 at 95%

    This screen shot from a spreadsheet I made illustrates why I think doing both may be beneficial based on analysis of my BigY BAM file.

    Notice that there are SNPs marked "unreliable" on not even listed by Yfull that received the highest ratings by FGC; and SNPs marked "Acceptable' by Yfull that are ranked 40% and 10% by FGC.

    Of the 27 shown, 20 SNPs receive top ratings from both FGC and Yfull. Thus over 25% of these SNPs rated highly (top 2 categories) by one entity wasn't given the highest two ratings by the other.
    Attached Images Attached Images
    Last edited by MitchellSince1893; 07-14-2015 at 05:07 AM.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
    37% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German, 3% Ireland, 3% Nordic, 2% French/Dutch, 1% India
    Hidden Content

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  8. #5
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    Very interesting--I just got some sample reports from FGC. I'll study them and see if they seem likely to help.

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    FGC will place the new novel named SNPs into ybrowse. Initially YFULL did not do this. YFULL may be fudging the reported STRs by using the results presented at FTDNA. Very curious how yFulll they can report a null425 event.
    Last edited by Cofgene; 07-13-2015 at 10:59 PM.

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    Quote Originally Posted by Cofgene View Post
    FGC will place the new novel named SNPs into ybrowse. Initially YFULL did not do this.
    That could be a real advantage. Thank you.

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    Quote Originally Posted by Cofgene View Post
    FGC will place the new novel named SNPs into ybrowse. Initially YFULL did not do this. YFULL may be fudging the reported STRs by using the results presented at FTDNA. Very curious how yFulll they can report a null425 event.
    It is also curious how YFull is able to report Y-GGAAT-1B07, which was never mapped to GRCh37. It has since been mapped to GRCh38 at Y:10687543-10687730

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    Both FGC and YFull analysis were highly useful to me to understand what FTDNA Big Y was doing and not doing as far analysis goes. FGC is explicit in showing how it removes the "widely shared" SNPs from delta to the reference sequence based on other data sets which I found useful to know exactly.

    The YFull interactive features to examine the raw data and also that of others who join a specific group is a big plus with YFull.

    FGC also provide data on private INDELs of which I have 6 that are higher reliability, two of which were verifiable by YSEQ Sanger. YFull does not report INDELs which could turn out to be useful.

    I also had, more importantly, a NGC Full Y at the BGI lab, and had YFull also analyze that. The value of the higher coverage and quality helps resolves the ambiguous cases from FTDNA Big Y data.

    I had 4 SNPs that were non high reliable in FGC analysis that I was able to verify by Sanger at YSEQ. YFull identified 3 as reliable and 1 as unreliable. Interestingly, FTDNA ranked two of them as medium quality.

    I am waiting on getting FGC data (from US lab) for a paper 12th cousin who is STR match, having failed twice--probably have to get new sample. This will be interesting case.

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  15. #10
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    I ordered an FGC analysis and if it proves to be useful will order for other project members. Thanks.

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