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Thread: Big Y changes

  1. #61
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    Quote Originally Posted by Mikewww View Post
    I've had a post mysteriously disappear. I must be politically incorrect.

    Any way, let us summarize the positive on the topic, which is Big Y and changes to it:

    Big Y is finally updating their on-line tools to include Big Y chromsome browsing and Terminal SNP guidance/matching.

    Big Y outsells their primary competition by 24 to 1 in P312 (according to Alex Williamson) and 16 to 1 in U106 (according to Charles Moore). P312/S116 is the giant Y haplogroup of Western and Central Europe.

    Big Y and FTDNA's SNPs in general are being converted to Hg38, which is needed.

    Big Y has sold for as low as $395 even though some pundits have said the enrichment costs alone were up to $400 so Big Y has apparently beaten the pundits predictions (as FTDNA told me privately they would).

    Big Y's $575 list price is too high and should be permanently reduced, in my opinion.

    Genetic genealogy is all about comparing people so the more people testing and in the database the better. The size of the matching database is important as well as other on-line functionality such as surname projects, geographic projects, STR matching and SNP guidance/matching (new). See the R1b FAQ page on genetic genealogy platforms for more info:
    https://www.familytreedna.com/groups/r-1b/faq#/FFTDNA
    What does these changes do for YFULL ?.............will we have a clash between BigY markers and YFull, I ask because my ftdna project works with Yfull people to find my line of new SNP's

    Father's Mothers Ydna ......R-S22778 ........Merlengo Veneto
    Father's Mtdna .....T2b17.......1735 Porcellengo Veneto Italy
    Wife's Ydna ..........R-DF99
    Sons Mtdna .....K1a4 ...........1710 Carnic Alps

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, A339+ )

    The main negatives = ( M193-, P322-, P327-, Pages11- , L25- , CTS1848- )

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  3. #62
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    I've looked at two different VCF zipped folders, one from last week (Hg19) and one from this week (Hg38). These were random selections so do not read any precision in to this. This is no statistical average of what we should expect.

    The Hg38 VCF provides about 35% more regions defined but not greater total coverage, perhaps even less.
    The Hg38 VCF gives 8.63 times the number of calls in the VCF file itself (763% increase)

    My opinion is this is about
    1) refining the coverage, weeding difficult (or difficult to read) regions AND
    2) dramatically increasing the number of SNPs called out in the VCF file itself.

    The VCF is really beefed up. The age of spreadsheets may be dwindling to support this and people using BAM files may already have a better personal infrastructure.

    However, I think this is really about FTDNA significantly enhancing support for its on-line functionality, the new Big Y Browser and Big Y SNP Terminal Guide. This will cause heartburn for some but all FTDNA is doing is providing more functionality - letting more project administrators participate more easily without the high powered computers. It's free so that's a not bad thing.

    Quote Originally Posted by vettor View Post
    What does these changes do for YFULL ? ...
    Submitting/resubmitting BAM files for interpretation or doing it yourself with the IGV BAM viewer is still there as an option. Do it yourself is not fun. I hope YFull will do a mass conversion of all of our BAM files to the Hg38 base so they can easily compare with new Hg38 based BAM files. I can see they might need to charge a re-interpretation fee if the current Hg19 customers want to send them our new Hg38 BAM files. It'll probably be worth it but I think the hassle is getting everyone to re-submit.


    ----------------------------------------------------
    VARIANTS.VCF (random example of new Hg38 VCF files)
    1st line:
    ##fileformat=VCFv4.1
    3rd line:
    ##reference=ucsc.hg38.fasta
    316,398 base pair locations called in the VCF file

    REGIONS.BED
    28,571 regions
    9,916,241 base pair locations covered

    ----------------------------------------------------
    VARIANTS.VCF (random example of old [last week] Hg19 VCF files)
    1st line:
    ##fileformat=VCFv4.1
    4th line:
    ##contig=<ID=chrY,length=59373566,assembly=hg19>
    36,675 base pair locations called in the VCF file

    REGIONS.BED
    20,863 regions
    10,638,843 base pair locations covered
    Last edited by Mikewww; 10-12-2017 at 07:10 PM.

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  5. #63
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    Looking through this thread it all seems overwhelmingly technical to someone like myself. I am not really sure this upgrade will make much difference to me. I currently have one match of 0 SNP difference ,but there is a difference between him and I according to a member of the E(Double helix) forum who deals with such things in that I am E-BY5220 +; which appears to be an individual SNP.
    Last edited by firemonkey; 10-12-2017 at 08:25 PM.
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  7. #64
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    Quote Originally Posted by firemonkey View Post
    Looking through this thread it all seems overwhelmingly technical....
    You are right, this can be technical. Anthrogenica has attracted very technical analysts and even a vendor and engineer or two.

    For for the technicians.

    I did a check against SNPs I've downloaded and converted to Hg38. The new VARIANTS.VCF file has greatly expanded what FTDNA calls the "known" variants list. This is good as that means we'll get actual ancestral calls for all of these "known" locations. We won't have to make as many assumptions about coverage from the REGIONS.BED file nor look at the BAM file.

    I am trying to determine what level or currency date these "known" variants are. The update is good but we really need VARIANTS.VCF's to be updated periodically with the new "known" lists as they are produced. I don't see that happening unless FTDNA wrote some kind of batch update program that does not dive into the full FASTQ files every update or reprocess the whole thing every update. The could have indexed the locations but I just think there are too many and the storage costs too great for that.
    Last edited by Mikewww; 10-12-2017 at 09:13 PM.

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  9. #65
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    Quote Originally Posted by Mikewww View Post
    Big Y outsells their primary competition by 24 to 1 in P312 (according to Alex Williamson) and 16 to 1 in U106 (according to Charles Moore). P312/S116 is the giant Y haplogroup of Western and Central Europe.
    Again, since this criticism is posting here, I'm going to respond. We've done a number of significant research projects, including one for one of the most prestigious labs in the US, if not worldwide. So, I'd keep that in mind. Incidentally, FTDNA was not selected for that project. Secondarily, FTDNA does a lot of good work and has made a number of important contributions, but I'll make this rebuttal, and exit. Edit: I've actually had good interactions with Bennett Greenspan in the past, myself, though I haven't interacted with him in the course of our business operations.
    Last edited by FGC Corp; 10-12-2017 at 09:35 PM.
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  11. #66
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    Quote Originally Posted by FGC Corp View Post
    Again, since this criticism is posting here, I'm going to respond. We've done a number of significant research projects, including one for one of the most prestigious labs in the US, if not worldwide. So, I'd keep that in mind. Incidentally, FTDNA was not selected for that project. Secondarily, FTDNA does a lot of good work and has made a number of important contributions, but I'll make this rebuttal, and exit. Edit: I've actually had good interactions with Bennett Greenspan in the past, myself, though I haven't interacted with him in the course of our business operations.
    In regards to the R-U106 Project, Greg Magoon and Iain McDonald have begun a dialog to hopefully include FGC results in Iain's analysis work sometime in the future. We recognize FGC results provide for a finer resolution than the Big Y test, but there are a bunch of technical and logistical hurdles which must be overcome. The biggest hurdle for Iain is simply the fact there is not enough hours in the day to accomplish all of his personal and professional tasks.
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  13. #67
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    Quote Originally Posted by Mikewww
    Big Y outsells their primary competition by 24 to 1 in P312 (according to Alex Williamson) and 16 to 1 in U106 (according to Charles Moore). P312/S116 is the giant Y haplogroup of Western and Central Europe.
    Quote Originally Posted by FGC Corp View Post
    Again, since this criticism is posting here, I'm going to respond....
    These are not criticisms. Those data points are posted on this FTDNA category thread where it is relevant to the topic of Big Y and its changes.

    These are just facts. This particular post doesn't even mention your name. You are drawing more attention to it yourself.

    Some people may take them as criticism but a piece of data is a piece of data and if it is posted in context of the thread I don't see the concern you have. If I posted those things over on your very own FGC thread I would have more empathy.

    Congratulations on your victories and I'm glad to see you posting as your singular self.

    Quote Originally Posted by Wing Genealogist View Post
    In regards to the R-U106 Project, Greg Magoon and Iain McDonald have begun a dialog to hopefully include FGC results in Iain's analysis work sometime in the future. ...
    It's another good point that I wouldn't have even brought up although I'm aware of it. I think only Big Y VCF results are included in Iain's free SNP age analysis.

    Genetic genealogy is all about comparisons so the databases methods and ease of sharing data are very important. Comparisons can only be done like for like.
    Last edited by Mikewww; 10-13-2017 at 03:45 PM. Reason: fixed grammar

  14. #68
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    I asked FTDNA today if they had any tutorials on the on-line Big Y Browser and Terminal SNP Guide.

    Here is the answer from their project admin support:

    Quote Originally Posted by FTDNA
    Please let everyone know that just because they can see something on the pages now, does NOT mean it's complete. They should please wait until the run is complete to work with the pages. Looking is okay but it may be a bit confusing at the moment. We did say 5-7 days and it's only been two-ish.

    And on the matching tab there's a link to the Learning Center piece on the updated Big Y.

    https://www.familytreedna.com/learn/...g/big-y/big-y/

    If you don't believe that gives enough information, let me know.

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    What I like about the guide is this:

    A person is considered a match if they have 40 or fewer differences in SNPs with you, and their haplogroup is downstream from your haplogroup or downstream from your four closest parent haplogroups.

    So hopefully what this means is an end to the e-mails saying I have a new Big Y match to people in random other haplogroups.

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  18. #70
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    Quote Originally Posted by Loderingo View Post
    What I like about the guide is this:

    A person is considered a match if they have 40 or fewer differences in SNPs with you, and their haplogroup is downstream from your haplogroup or downstream from your four closest parent haplogroups.

    So hopefully what this means is an end to the e-mails saying I have a new Big Y match to people in random other haplogroups.
    If I'm interpreting that right, then people who are 3 SNPs down from M222 would get 'matched' with the whole of M222 and probably Z2961 too? But those down in the pits of DF97 would get matched with others in sub-branches of DF97 only.
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