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Thread: Big Y changes

  1. #701
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    Quote Originally Posted by Cassoulet View Post
    Ok if it's just that, why is it a new major version the 6.01 instead of the 5.10 ? They must have added something else or maybe not.
    I’m afraid you’ll have to ask them that. If you’re interested you can join their Facebook Page, to keep up with what they’re doing.

    https://www.facebook.com/groups/yfull/
    Last edited by JMcB; 01-05-2018 at 04:44 PM.

  2. #702
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    Quote Originally Posted by JMcB View Post
    While taking a look at your branch, I was reminded of what a nice job YFull has done with their tree format. The flags are a nice touch. By the way, their new tree was released today.
    YFull has already converted to build HG38. And YFull shows the chromosome position of a quiried SNP for both HG19 and HG38 builds.
    FTDNA Big-Y SNP Results: R1b-U152+, L2+, Z367+, Z384+, L20+, CTS9733+, BY34096+

    Milam / Mileham / Milum Y-DNA Surname Project
    Hidden Content

    My Avatar is an image of my family history website's home page: Hidden Content
    An history of Thomas Milam (1738) and his 6 sons as found in Virginia court records from 1738 - 1820.

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  4. #703
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    Quote Originally Posted by Celt_?? View Post
    YFull has already converted to build HG38. And YFull shows the chromosome position of a quiried SNP for both HG19 and HG38 builds.
    Yes, I know. All they need now, is to start getting some new Bam files coming in.

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  6. #704
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    Quote Originally Posted by Cassoulet View Post
    Ok if it's just that, why is it a new major version the 6.01 instead of the 5.10 ? They must have added something else or maybe not.
    I believe the major version changes with the year.

  7. #705
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    I have checked SNP reports for all SNPs with Big Y origin and I have found several bugs:

    1. Many indels are reported as derived while they are not.
    Examples: BY11750, BY18729, BY22302, BY27761, BY3070, FGC17059, FGC5795, L136, Y4922, Z2065

    2. Some SNPs are reported as derived while they are not and vice versa
    CTS4437, CTS5884

    3. YSC0000227 is still on the FTDNA haplotree defining haplogroup P
    It was removed from ISOGG haplotree in December 2016 because it has reverse ancestry/derived values (A->G) and was replaced by M1264 on the same position with G->A mutation.

    4. Inconsistent variant reporting
    Variants reported as "+" on the haplogroup screen and in the SNP file, but "-" in the BigY results.

    CTS3101 (kits 348785, 350685)
    Files
    348785_SNPs_20180105.csv
    350685_SNPs_20180105.csv
    contain:
    "CTS3101","True","Big Y"
    On the haplogroup screen is result CTS3101+
    Files
    348785_BigY_Data_20180105.csv
    350685_BigY_Data_20180105.csv
    contain:
    "Known SNP","CTS3101","CTS3101","No (-)","Yes","G","G","High"

    File
    195364_SNPs_20180106.csv
    contains
    "Z18012","True","Big Y"
    On the haplogroup screen is result Z18012+
    File
    195364_BigY_Data_20180106.csv
    contain
    "Known SNP","Z18012","Z18012","No (-)","Yes","T","T","High"

    5. Wrong named variant position
    For SNP A5013, FTDNA shows in their BAM browser Position 8766127.
    http://ybrowse.org/gb2/gbrowse/chrY/?name=A5013 shows position 8766097
    I suppose YBrowse will have the right position for "A" SNPs

    6. I'm not able to find a few SNPs on the haplotree

    I have reported all bugs to FTDNA so we will see.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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  9. #706
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    Here is a blogger article on the "new" Big Y.
    https://dna-explained.com/2018/01/12...-results-hg38/

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  11. #707
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    Quote Originally Posted by Mikewww View Post
    Here is a blogger article on the "new" Big Y.
    https://dna-explained.com/2018/01/12...-results-hg38/

    I think she did a nice job of explaining everything and mades some good points.

    For example, the following point. Especially, considering that FT had sold Big Y for years under the premise that it was meant to explore “deep ancestral links”.


    “One of the benefits of the Big Y, previously, was the ability to view people of other surnames who matched your SNP results. This ability to peer back into time informed us of where our ancestors may have been prior to where we found them. While this isn’t genealogy, per se, it’s certainly family history.

    A good case in point is the Scottish clans and how men with different surnames may be related. As a family historian I want to know who I match on my terminal SNP and the direct upstream SNPs so I can walk this line back in time.“


    She also makes a good point about the lack of visibility.


    “What you don’t receive today, that you did receive before, is a comprehensive list of who you match on your terminal and upstream SNPs.

    For example, I was working with someone’s results this week. They had no matches ... However, when I went to the relevant haplogroup project page, I discovered that indeed, there are at least 4 additional individuals who do share the same terminal SNP, but the tester would never know that from their Big Y results alone, if they didn’t check the project results page.

    Of course, it’s unlikely that every person who takes the Big Y test joins a Y DNA project, or the same Y DNA project. Even though projects will show some matches, assuming that the administrator has the project grouped in this manner, there is no guarantee you are seeing all of your terminal SNP matches.

    Project administrators, who have been instrumental in building the tree can also no longer see who matches on terminal SNPs, at least not if they are separated by more than 30 mutations. This hampers their ability to build the Y tree.”


    As a case in point, under the old system I could see the two people who shared my Terminal SNP. Which had only just recently been split out of another branch. When those two matches came in, I asked them to join our Z140 Project, which both of them did. With one of them bringing a relative along with him. I later asked them if they would submit their Bam files to to YFull. Which thankfully, they also did. So now our branch is viewable at YFull, in a manner that is far more informative than what you see at FTDNA. It also got me started asking others to join our Project, so there are now ten more people in our subgroup, that weren’t there before.

    The problem is, I can no longer see any matches. So if we took our tests today, all of that information would’ve been lost. Ten people wouldn’t have join the Z140 Project, denying my Administrator the extra data. Three wouldn’t have gone to YFull, denying YFull the extra data. Which would have denied me a lot of information, that I’ve found to be very useful and have been able to pass on.



    Fortunately, I think her suggestions - if Family Tree takes her advice - may go a long way towards remedying some of the problems.


    “Here’s a list of changes and updates I’d suggest to improve the new hg38 Big Y experience:

    In addition to threshold matching, an option for direct SNP tree matching through the 5 SNPs shown on the participant’s 5 step mini-tree, purely based on haplotree matching. This second option would replace the functionality lost with the 30-mutation threshold matching today.

    A matches map of the most distant ancestors at each level of matching for both threshold matching and SNP tree matching.

    An icon indicating whether a Big Y match is an STR match and which level of STR panel testing the match has completed. This means that we could tell at a glance that a Big Y match has tested to 111 markers, but is only a match at 12.

    An icon indicating if the Big Y match has also taken the Family Finder test, and if they are a match.

    An icon on STR matches pages indicating that a match has taken a Big Y test and if they are a match.

    Ability to query through the Big Y browser to SNP locations not on the list of named or unnamed variants.

    Age estimates for haplogroups”.
    Last edited by JMcB; 01-13-2018 at 08:01 PM.

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  13. #708
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    Quote Originally Posted by JMcB View Post
    I think she did a nice job of explaining everything and mades some good points.

    She also makes a good point about the lack of visibility.

    “What you don’t receive today, that you did receive before, is a comprehensive list of who you match on your terminal and upstream SNPs.
    ...
    Project administrators, who have been instrumental in building the tree can also no longer see who matches on terminal SNPs, at least not if they are separated by more than 30 mutations. This hampers their ability to build the Y tree.”
    https://dna-explained.com/2018/01/12...-results-hg38/

    It's too bad more project administrators did not provide feedback on the positive parts of the old matching system. We should have realized that FTDNA would make changes because of the extreme criticism they received on the old Big Y Matching system about how worthless the old system was because it was too wide open. I could dig up some quotes from some very large haplogroup project admin's talking about the old Big Y matching should be ignored, but that would be of no use.

    This is the Goldilocks and the Tree Bears problem where some like the soup hot, some lukewarm, etc. This is why I requested a second version of the Big Y matching, but this one tailored for project admin tree research. If anyone wants to refer to this in discussions with FTDNA here is the request information:

    Request ID: 723906 01Dec2017
    Update Big Y matching to have better qualified variants (only) in the mismatch counting AND
    Add a 2nd function for the GAP tool only that searches for Big Y results to support broader tree research
    Last edited by Mikewww; 01-17-2018 at 04:34 PM.

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  15. #709
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    The Hg38 conversion project is working!

    It is clear that FTDNA has re-evaluated SNP results and branching across the haplotree as a part of this project.

    Hg38 has enabled them to be more confident in variant calls. This has uncovered some new variants, but more importantly has increased FTDNA's aggressiveness in calling more variants as reliably derived and culling out marginal calls. At the same time, we've seen an acceleration of Big Y testers.

    I just ran through the R1b-M269>L23>L51>L151>P312>Z290(and L21) haplotree and compared it what I had archived on October 9th, right before the Hg38 conversion started.

    The number of distinct branches in L21 increased over the last four months by 9.1%, from 2,034 to 2,220.

    The total number of SNPs on the L21 tree increased by a whopping 24.7%, from 7,909 to 9,859. L21 is closing in on 10,000.

    (for reference) DNAexplained article on Hg38 and the new functions in Big Y:
    https://dna-explained.com/2018/01/12...-results-hg38/

    P.S. Nothing is perfect nor ever will be save one, but a lot of progress has been made without upcharges or subscriptions for existing Big Y testers. It's been a long time coming, that's for sure.
    Last edited by Mikewww; 02-12-2018 at 09:44 PM.

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  17. #710
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    According to my observation, there are the following reasons for more SNPs and branches:

    1. Many new SNPs in unstable areas that cannot be verified by Sanger sequencing - in PAR, DYZ19, palindromes, centromere... I'm not sure that all of them are real.

    3. Some new SNPs are caused by the new aligning, so for the already known mutation, there are new names and the three contain both old (not existing in hg38 data) and new SNPs, as an example, YP1037 old is BY29713 new, but branch R-YP1017 contains both of them, YP1037 is always no call.

    3. Some of the new branches are just a consequence of more test results and are not related to the hg19->hg38 conversion.

    In my 11 kits, I saw after the hg19->hg38 conversion no new SNP that could be verified by Sanger sequencing.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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