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Thread: How to submit Y-SNP to ISOGG/Ybrowse

  1. #1
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    How to submit Y-SNP to ISOGG/Ybrowse

    I think the title is clear.
    E-M84>FGC18389>FGC18413>FGC18401>FGC18422>Y99171 tMRCA 2550ybp

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  3. #2
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    There are coordinators for each haplogroup on the ISOGG tree web pages. I would work with them. Ray Banks is the leader for the whole thing, but the processes may vary somewhat by haplogroup (coordinator).

    It is difficult for a volunteer system to keep up with all of the changes at the youthful levels of branching.

  4. #3
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    This appears to be the most recent discussion on how to get novel SNPs to ISOGG. I just got my VCF file on YFull and have 29 novel SNPs assigned a "y," which I'm told means they'll eventually end up on ISOGG somewhere sometime in the future.

    Do I need to help in this or is it something that ISOGG and YFull handle themselves? Or do I do nothing until Family Tree hands out our BAM files that're already overdue? My YFull results read "R-P312*, R-DF27*, R-Z2573*, R-Z37492*, R-Z2559*, R-Z2552*, R-DF83*" and I'm told the asterisks have a different meaning at YFull than elsewhere. Is this technically an incomplete result until I get my BAM file to them?
    "Bid me discourse, I will enchant thine ear..."

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    If you do a search for your novel SNPs on ISOGG YBrowse you will see that YFull has submited them to the database.

    http://ybrowse.y-chromosome.org/gb2/gbrowse/chrY/?

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    The first step is to register your YSNP mutations and labels to YBrowse. Our lead admin for L226 has now submitted over 1,000 YSNPs to his database.

    The second step is to ensure that FTDNA has your part of the haplotree in sync with your view. Michael Yager at FTDNA is being very responsive and proactive to getting the FTDNA haplotree reflective of the admin's research these days. Out of 72 branches, we now have no extra unwanted branches and are only missing one branch discovered by YSEQ testing.

    Third, determine which organization supports your particular haplogroup and get your VCF files uploaded for analysis. For R1b, that means uploading your files to the common NGS test database. For R-U106 (part of R1b) and R1a, also submit you files to YFULL. A lot of haplogroup I submits to YFULL as well.

    The haplotree at ISOGG is no longer very relevant for haplogroup R and we have not been submitting our branches there for several years. First, they will not accept many of our branches since they are too young. Second, they amount of data that they want is too burdensome to bother with. Third, their haplotree compared to FTDNA, BigTree and YFULL is so far behind in functionality, it is no longer relevant for R1b.

    Your title may be clear - but the haplogroup under consideration really influences your choices.

  7. #6
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    Quote Originally Posted by RobertCasey View Post
    The haplotree at ISOGG is no longer very relevant for haplogroup R and we have not been submitting our branches there for several years. First, they will not accept many of our branches since they are too young. Second, they amount of data that they want is too burdensome to bother with. Third, their haplotree compared to FTDNA, BigTree and YFULL is so far behind in functionality, it is no longer relevant for R1b.
    At the ISBA conference currently underway in Jena, David Reich closed his presentation with an invitation to submit SNPs that should be searched for in aDNA. They are currently updating the capture reagent that they use, and it will be available for others to use. With regard to the Y chromosome, I find it disturbing that they are still using the far-behind, no-longer-relevant-for-R1b ISOGG tree as their SNP bible. I'll just post that slide, as tweeted this morning by Alexander M. Kim, and hope somebody with a geographically broad outlook can clue them in on what they should be looking for. Source -- https://twitter.com/amwkim

    Screen Shot 2018-09-19 at 8.58.54 AM.jpg

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