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  • A hobbyist plea

    I started in 2004 with the Shetland project administered by David Faux, then later the Deep Clade test along with 67 markers. Back end of last year I did the 23andMe mainly for the health report, then took the plunge to do the Big Y. Even with this background I am very much a simple hobbyist and the pace of the findings are increasing at an alarming rate. It does seem that the Big Y is perhaps a step too far.

    Now CTS4179+ with negative on the three known subclades. However, it has thrown up an interesting dilemma in that I simply ……… don’t fit in!!! ………. but I knew that

    I am a retired accountant with a phd. In teaching accounting my aim was always to find ways to simplify a student’s path through the accounting maze. I have also spent a lot of my time programming interactive learning materials – so with the combination of the two, I am quite happy dealing with numbers/logic.

    My plea:

    I would find it helpful if someone could describe the initial process required to link values in the vCard file to SNPs. Is there a comprehensive listing of these two figures?

  • #2
    Most (but not all) Y-SNPs are in the Ybrowse database.

    Comment


    • #3
      Thanks for that link. I have been there before but still don't know how it works. Clearly, not for the hobbyist.

      Comment


      • #4
        Hi. I think what you are asking is can you take a position from your BigY data and find out what if any named SNP exists at that location?

        If so Ybrowse as mentioned above is your best bet.

        How to do it.

        In the Landmark or Region input box type

        ChrY:

        then without a space enter the area you are looking for. Example.

        22157311

        You don't need the comma's the system will place these for you.

        then type

        ..

        then type the position 22157311 again.

        So your final input will look like

        ChrY:22157311..22157311

        Hit the search button.

        Your search will be reformatted to look like

        ChrY:22,157,311..22,157,311

        If you look down at the SNP section of the details box it will tell you the name(s)of the SNP at that position.

        Many of the novel variants in your BigY results have not yet been named so nothing will appear for many searches under the SNP section but you will be surprised at how many of your 'novels' may turn out to be known SNP's.

        I was not 100% sure what it was that you were trying to do so apologies in advance if I answered the wrong question.

        Earl.

        Comment


        • #5
          The Hobbyist wrote "Now CTS4179+ with negative on the three known subclades.

          The question that came to my mind on this is are you a confirmed negative or is it that you are just not a
          good positive for those three SNPs

          The BigY has some issues with saying negative on a SNP
          when it is "maybe a positive and maybe not"
          If it is the case the test is not clear one way or the
          other you need a better test - or prior to that a
          different analysis.
          You can get the different analysis a yfull.com
          and they have a browser that will allow you look
          as a SNP and see what the raw data says about it.
          You will need to request your BAM file from FTDNA
          and send the link to yfull.com
          The do want money for this - see the web site for details.

          If there is any doubt on any one of those three SNPs
          you can check with yseq.com and see if the SNP is in
          their inventory. That will tell you for sure.

          If you do not wish to pay the yfull.com price you can
          then use the various free browsers to look at your BAM file yourself
          That is in the advanced hobbyist, league to which I think
          you should aspire, IMHO
          There is help for them on line
          If you need more on any of these ideas just ask here

          Comment


          • #6
            Earl,
            Thanks for the reply. Yes, that's what I was wanting. Have been on that URL before, but it didn't make any sense to me.

            I suppose that I was also hoping that someone had a NICE list of all the SNPs and their corresponding chrY id.

            Thanks again.

            John

            Comment


            • #7
              JWS,

              When looking into ordering the Big Y, I planned to send my bam file to yFull. It was part of the overall budget.

              My main plea was to those with experience, to tell me simply "How they arrive at a SNP for a given chrY id". Then there is the issue for new SNPs not on ISOGG. "How do they keep a record of these".

              I just want a simple "Janet and John" explanation similar to that given by Earl above.

              John

              Comment


              • #8
                The problem is that SNPs are being found daily and named
                by each company as they find them
                ISOGG is trying to keep up but they cannot as things are
                added with each new BigY/Yfull/FGC kit they process

                This area is so new that there will be turmoil for a while
                yet.
                My point is that given you have a solid SNP at one level
                and then the next level down you have no SNPs for 3 candidates
                While that could be true it must be confirmed true by
                looking at those 3, one by one, in all the data files
                even back to the BAM files.

                Comment


                • #9
                  Big Y

                  I do have a "nice" list of variants I can send you.

                  Email me at [email protected].

                  I am the co-admin of the Clan Donald project,
                  which has lots of CTS4179 people (most L176.1+ however.)

                  Comment


                  • #10
                    Hi,

                    Thanks for the kind offer.

                    An email is on it's way.

                    John

                    Comment


                    • #11
                      JSW,

                      I received my bam file yesterday and sent the link to yFull.

                      BUT, I am still keen to learn a little about the processes - so I can try to keep pace. Otherwise I will be left behind - not something I would want.

                      John

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