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Thread: Big Y changes

  1. #1
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    Big Y changes

    Well, we've all waited for this a very long time:

    http://mailchi.mp/familytreedna/big-...7?e=9dec88d3cc

    The wording is somewhat curious, it's not clear for me if these futures are only usable personally, or also for admins. It seems some things will be useful but while I understand why they go to HG38, I'm also worried by potential confusion it will cause. Hopefully others will follow.

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  3. #2
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    Yesterday noticed at FTDNA my terminal snp YP6291 was changed to FGC59403 which is according to Yfull is YP6292. FGC59403/YP6292 is among the defining snps on the Yfull tree but not the terminal snp, YP6291 is. Looks like part of the pending changes. Since I posses both snps, it doesn’t matter concerning the designation, but whose defining snp should one list as the confirmed terminal?

  4. #3
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    Just received an email on this being addressed as a customer vs the previous posting of being an admin.

    Dear Big Y Customers,

    We've been quietly working on some big updates to Big Y, and want to give you a first look before the release goes live, October 10th!

    Once the release is live, we will be recalculating Big Y matches. We anticipate this taking approximately 5-7 days. During this time, you will see "Results Pending" in the Big Y section. You will be notified by email once your results are processed and ready.
    ...
    The rest of the email reads the same as the admin version.

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    So what will it mean more matches? Less matches? and how reliable will it be? I get the impression experts aren't hugely impressed with the Big Y interpretations in terms of accuracy and detail.

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    The change from Hg19 to Hg38 includes an update of the Y chromosome sequence and means that all existing spreadsheets which include SNP locations will need to be updated to reflect the new coordinates and all Private Variants will change. I assume that new sequence may also involve a change in the reference values at certain locations which could result in changes to the derived value for some SNPs. My main concern as one who includes BAM file analysis to confirm results at each Variant is being able to update the 50 or so existing BAM files that I have, or to obtain updated files from FTDNA without having to chase up the individual candidates for them. Another problem for us is that as far as I can tell, YBrowse only works with Hg19.If this is the case, and isn’t updated to include a Hg38 option, looking up locations will involve a backwards transition from Hg38 to Hg19.

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    European - 99.2%............Central Asian - 0.8% .............Yfull - 1460BC
    Father's Mtdna .....T2b17.......1735 Porcellengo Veneto Italy
    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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    Quote Originally Posted by Muircheartaigh View Post
    Another problem for us is that as far as I can tell, YBrowse only works with Hg19.If this is the case, and isn’t updated to include a Hg38 option, looking up locations will involve a backwards transition from Hg38 to Hg19.
    Similarly: Will YFull be able to handle Hg38 BAM files? Even if so, FTDNA's announcement--together with FTDNA's recent eagerness to define new subclades from Big Y results--may make YFull's analysis less important than it has been up until now.

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    Quote Originally Posted by lgmayka View Post
    Similarly: Will YFull be able to handle Hg38 BAM files? Even if so, FTDNA's announcement--together with FTDNA's recent eagerness to define new subclades from Big Y results--may make YFull's analysis less important than it has been up until now.
    Hopefully FTDNAs decision will be a catalyst for others such as Full Genomes Corp. Yfull and Yseq to change. It would be chaos to have the different companies operating with differing standards, particular in the case of variants without a SNP label assigned to them including all of the Tens of thousands Private SNPs currently in the System. They will now all need to be reassigned the new locations defined by the Hg38 Sequence.

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  16. #9
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    Quote Originally Posted by lgmayka View Post
    Similarly: Will YFull be able to handle Hg38 BAM files? Even if so, FTDNA's announcement--together with FTDNA's recent eagerness to define new subclades from Big Y results--may make YFull's analysis less important than it has been up until now.
    it is more likely that due to the Yfull team having found many new results that Ftdna needs to "catch up"

    European - 99.2%............Central Asian - 0.8% .............Yfull - 1460BC
    Father's Mtdna .....T2b17.......1735 Porcellengo Veneto Italy
    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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  18. #10
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    Quote Originally Posted by vettor View Post
    it is more likely that due to the Yfull team having found many new results that Ftdna needs to "catch up"
    In my experience, as far as my group is concerned, Yfull hasn’t revealed anything that wasn’t available from analysis of the BAM files provided by FTDNA but I agree that the Big Y results as they are currently presented are an enigma to most participants.

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