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A SNP by Any Other Name

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  • A SNP by Any Other Name

    When checking your Big Y results, be sure to exhaust the alternate names for SNPs, because not all SNPs appear under the most familiar name. DF13, for example, which comprises about 95% of R-L21, is not listed by that name in Big Y but is known as CTS241.

    When searching for particular SNPs, it seems to me, it is best to choose "Show All" from the drop-down menu in the second column from the left ("Derived?"). Then a search will show you positive, negative, and "no-call" results.

    You can use ISOGG's Trees and its SNP Index to see what the possible alternative SNP names are:

    http://www.isogg.org/tree/index.html

    http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html

    Of particular interest to me is DF41 (the defining SNP for my own subclade). It too is not listed in Big Y by that name but is known as CTS6581. DF41 and CTS6581 are different names for the same SNP. A second, different SNP, but currently thought to be approximately equivalent to DF41/CTS6581, is CTS2501. It's included in Big Y, as well.
    Last edited by Stevo; 16th March 2014, 02:20 PM.

  • #2
    An option to search by SNP position would also help.

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    • #3
      Originally posted by Ann Turner View Post
      An option to search by SNP position would also help.
      That's a good idea. Apparently thus far one can only search by the name of the SNP, except for the "Novel Variants", which, naturally, have not been named yet.

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      • #4
        Originally posted by Stevo View Post
        That's a good idea. Apparently thus far one can only search by the name of the SNP, except for the "Novel Variants", which, naturally, have not been named yet.
        I've posted this elsewhere but as an example, in my comparisons I translate CTS6581/DF41/S524 to 16992602T>C.

        In this day, the profusion of SNP labels is alphabet soup anyway so you can get a true unique identifier by going right to the GRCh37/hg19 position number and allele changes.

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        • #5
          Originally posted by mwwalsh View Post
          In this day, the profusion of SNP labels is alphabet soup anyway so you can get a true unique identifier by going right to the GRCh37/hg19 position number and allele changes.
          Well, except for the ones that read in one direction on Chromo2, and another on several other test platforms. In a few cases there is a different allele read (at the same position) for a different "strand," or whatever the chip is reading. Dr. Jim Wilson has explained it, but it's over my head -- or anyway over a place to which I have any desire for my head to go. This problem may be limited to marker positions that are palindromes, and/or indels. If so, they can probably be flagged, but I expect that will become necessary.

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          • #6
            Originally posted by razyn View Post
            Well, except for the ones that read in one direction on Chromo2, and another on several other test platforms. In a few cases there is a different allele read (at the same position) for a different "strand," or whatever the chip is reading. Dr. Jim Wilson has explained it, but it's over my head -- or anyway over a place to which I have any desire for my head to go. This problem may be limited to marker positions that are palindromes, and/or indels. If so, they can probably be flagged, but I expect that will become necessary.
            You are right. It has to do with how that version of Illumina reads the DNA. Unfortunately that means I do them last as far as integration goes. It's really already done for L21 though in the file I posted, because ISOGG Ybrowse has the allele changes correct so I just need to get the list of S series and then glean the alleles from Ybrowse.

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            • #7
              Yeah, it's just reading from the opposite side (or strand) of the double helix. Since A is always opposite T, and G is always opposite C, it's not too hard to spot.

              Take the location and nucleotide change for DF41/CTS6581:

              16992602T>C

              Read from the opposite side of the double helix, the change would be A>G.

              It is kind of a pain, though.

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              • #8
                "An Indel by another location"

                I'm looking at indels. Since I don't have any bam files
                yet, could somebody describe EXACTLY how the locations
                of indels in the vcf file corresponds to how they
                are located in the bam file (number is end, beginning, etc.)
                as well as as they are listed on the ISOGG list?

                Comment


                • #9
                  DF13, for example, which comprises about 95% of R-L21, is not listed by that name in Big Y but is known as CTS241.
                  CTS241 does not show up in my Big Y result even though I have tested positive for it in al la carte order ?

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                  • #10
                    Originally posted by Brunetmj View Post
                    CTS241 does not show up in my Big Y result even though I have tested positive for it in al la carte order ?
                    You will need to examine carefully the bam and vcf files
                    to see what is there. You may have to look it up on
                    ybrowse at isoggg.org.

                    But even that may fail. You may need to look at the
                    bam file.

                    I have found errors that way. This includes all sorts
                    of errors, not just BigY web page results errors.
                    It includes an error in a $39 test.

                    Doug McDonald

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                    • #11
                      [QUOTE]You will need to examine carefully the bam and vcf files
                      to see what is there. You may have to look it up on
                      ybrowse at isoggg.org./QUOTE]

                      Would that mean just me or for everyone who is DF13? Or to reframe my questions does CTS241 show up in some folks main results and not others?
                      Or was Stevo taking about this SNP buried in the vcf files?

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