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  • Mapping positions to SNP names is hard work

    Am hoping someone who has knocked down this brick wall will share ways of doing so.

    Have recently spent many hours trying to take my Big-Y 'novel variants' and map them against existing SNP names and variants.

    The best example to offer is that of the SNP DF100. Even at ftDNA there are discrepancies so for us home researchers it is simply very challenging. Re DF100, ftDNA sell an SNP test that tests for it (am +ve) and lists this in the SNPs page in one's login. But DF100 is not listed in Big-Y. another poster here smilligan, helped out by suggesting searching my Big-Y novel variants for pos '16775613' and sure enough that is there and +ve.

    1) Am wondering why DF100 can be listed in our SNP page but is not listed in Big-Y

    2) In my Big-Y results are 138 novel variants. I started taking them 1 by 1 and trying to find known names. Again smilligan kindly supplied an xls file with many SNP name to y-pos matches, but of the 1st 20 I tried to identify there were no matches and it is a very slow time consuming task.

    Are any other people able to point out ways to map y-pos numbers (novel variants) to any established names & aliases ?. If so this input should help many other people trying to do this.

    The one that now has me stumped is, what is the y-pos for CTS655 (L753, YSC0000083).

    DSM

  • #2
    Go here:

    http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/

    And put in the "Landmark or Region" box: CTS655

    Human Y Chromosome: 1 bp from ChrY:6,931,040..6,931,040

    It's the unnamed SNPs that are going to be fun.

    Comment


    • #3
      Check ISOGG

      Hi,

      The top of the ISOGG SNP INDEX page has a link to a really big file with positions.
      http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html

      Originally posted by dsm View Post
      ...
      Have recently spent many hours trying to take my Big-Y 'novel variants' and map them against existing SNP names and variants....
      DSM

      Comment


      • #4
        Originally posted by dsm View Post
        Am hoping someone who has knocked down this brick wall will share ways of doing so.

        Have recently spent many hours trying to take my Big-Y 'novel variants' and map them against existing SNP names and variants.

        The best example to offer is that of the SNP DF100. Even at ftDNA there are discrepancies so for us home researchers it is simply very challenging. Re DF100, ftDNA sell an SNP test that tests for it (am +ve) and lists this in the SNPs page in one's login. But DF100 is not listed in Big-Y. another poster here smilligan, helped out by suggesting searching my Big-Y novel variants for pos '16775613' and sure enough that is there and +ve.

        1) Am wondering why DF100 can be listed in our SNP page but is not listed in Big-Y

        2) In my Big-Y results are 138 novel variants. I started taking them 1 by 1 and trying to find known names. Again smilligan kindly supplied an xls file with many SNP name to y-pos matches, but of the 1st 20 I tried to identify there were no matches and it is a very slow time consuming task.

        Are any other people able to point out ways to map y-pos numbers (novel variants) to any established names & aliases ?. If so this input should help many other people trying to do this.

        The one that now has me stumped is, what is the y-pos for CTS655 (L753, YSC0000083).

        DSM
        Yes, this is needlessly complicated.

        I'm not sure how your xls file from smilligan is structured, but Excel's VLOOKUP function might be able to automate your searches.

        Have you tried Felix's utility? It might not get you exactly what you're looking for, but it will be informative.

        https://chrome.google.com/webstore/d...doediffhcdfdmj

        Comment


        • #5
          Originally posted by Paulie View Post
          Go here:

          http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/

          And put in the "Landmark or Region" box: CTS655

          Human Y Chromosome: 1 bp from ChrY:6,931,040..6,931,040

          It's the unnamed SNPs that are going to be fun.
          Does FTDNA have its own accessible registry of SNP labels and position numbers? I took several of the "known" SNPs on the Big Y results screens that I didn't recognize them and plugged them into the Ybrowse tool. Ybrowse didn't recognize them. I'm sure its more than just PF series SNPs, but those seem to be among the most problematic to find in Ybrowse.

          FTDNA has to have an index that they use to correlate SNP positions and changes to every label they use in the "Known" SNPs group. Where is it? I feel like I'm missing something.

          Do we have to go other sources, i.e. some registries that Chris-Tyler Smith (CTS) or Paulo Francalacci (PF) for these? There are a good 20-30 sets of initials used by the various labs.

          Comment


          • #6
            I have a file of named SNPs, Indels, and STRs from various sources that I could share. Its based on one I got from Krahn
            but includes many more, including the S ones.

            That's not the problem. The problems are assigning them,
            and that some are off by one from what BigY uses.
            It will do any reasonable number of file pairs at once.
            Output can be massaged in Excel to send to a network program, again not terribly friendly.

            I wrote a program to do it and it works great. I also
            tried sharing it but it is apparently terminally user
            unfriendly. Source code available if you are adept
            at that. Its plain C and SHOULD just run on any OS,
            as its a command line program. You would need the bed and vcf files.

            HOWEVER, its tiny, tiny, and should be adaptable to the Web
            for doing just one or a few file(s) by those who are adept at that ... which
            is not me. The user would upload bed and vcf, it would return this.
            HELP WANTED.

            Oh yes, off topic: yes, the bam file download is fixed.
            Last edited by dtvmcdonald; 7 April 2014, 06:35 PM.

            Comment


            • #7
              Thanks

              Originally posted by Paulie View Post
              Go here:

              http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/

              And put in the "Landmark or Region" box: CTS655

              Human Y Chromosome: 1 bp from ChrY:6,931,040..6,931,040

              It's the unnamed SNPs that are going to be fun.
              Thanks for that - I had been to that site several times but had no idea how to drive it. So simple once it is explained. Thankyou - very much appreciated.

              Doug M
              (L11*/P310*)

              Marker/Marcher project.

              Comment


              • #8
                Thanks all others

                To everyone else who posted. Thanks.

                As further feedback I contacted my DNA mentor (Debbie Kennett) and discussed this problem with her. Debbie suggested that ISOGG was working on a solution (but unfortunately don't have my novel variants there yet).

                Deb's link (also one I had previously found) was to ...
                http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html

                I don't know if we can feed this site with what we have as there has to be an issue of veracity of data.

                Doug M.

                Comment


                • #9
                  Reverse look up works as well

                  Originally posted by Paulie View Post
                  Go here:

                  http://ybrowse.isogg.org/cgi-bin/gb2/gbrowse/chrY/

                  And put in the "Landmark or Region" box: CTS655

                  Human Y Chromosome: 1 bp from ChrY:6,931,040..6,931,040

                  It's the unnamed SNPs that are going to be fun.
                  Having had great success following this I had a go at using it to convert a ChrY pos into a known SNP name & it worked. The trick is to format the pos data correctly i.e. I know that 15697457 is the ChrY post for CTS4528 (one of my SNPs). So in the 'Landmark or Region' box I entered ChrY:15697457..15697457 and sure enough after clicking search it came up with the position and the names CTS4528 and S1200. This has really been a great help.

                  Doug Marker

                  Comment


                  • #10
                    This site may be helpful:

                    http://www.ncbi.nlm.nih.gov/snp/limits

                    This database may be a holdover from they days when this was a science, and new SNPs were shared and not protected by patents or copyrights. All I see are rs numbers...

                    They do report only around 184,000 Y- SNPs, though...

                    Comment


                    • #11
                      Originally posted by hansonrf View Post
                      This site may be helpful:

                      http://www.ncbi.nlm.nih.gov/snp/limits

                      This database may be a holdover from the days when this was a science, and new SNPs were shared and not protected by patents or copyrights. All I see are rs numbers...

                      They do report only around 184,000 Y- SNPs, though...
                      Just fixed the wording...

                      Comment


                      • #12
                        Originally posted by dsm View Post
                        Am hoping someone who has knocked down this brick wall will share ways of doing so.

                        Have recently spent many hours trying to take my Big-Y 'novel variants' and map them against existing SNP names and variants.

                        The best example to offer is that of the SNP DF100. Even at ftDNA there are discrepancies so for us home researchers it is simply very challenging. Re DF100, ftDNA sell an SNP test that tests for it (am +ve) and lists this in the SNPs page in one's login. But DF100 is not listed in Big-Y. another poster here smilligan, helped out by suggesting searching my Big-Y novel variants for pos '16775613' and sure enough that is there and +ve.

                        1) Am wondering why DF100 can be listed in our SNP page but is not listed in Big-Y

                        2) In my Big-Y results are 138 novel variants. I started taking them 1 by 1 and trying to find known names. Again smilligan kindly supplied an xls file with many SNP name to y-pos matches, but of the 1st 20 I tried to identify there were no matches and it is a very slow time consuming task.

                        Are any other people able to point out ways to map y-pos numbers (novel variants) to any established names & aliases ?. If so this input should help many other people trying to do this.

                        The one that now has me stumped is, what is the y-pos for CTS655 (L753, YSC0000083).

                        DSM
                        Not sure if this what you are looking for.

                        Try this: YSNP Novel Variants

                        Comment


                        • #13
                          Originally posted by felix View Post
                          Not sure if this what you are looking for.

                          Try this: YSNP Novel Variants
                          Hi Felix
                          I had contacted you for directions for the directions for the 23andme to Y search.. You did give me the link but I am pretty dumb about computers.. I have Google Chrome but what else do I need?

                          You were kind enough to do my grandson's for me.. I also have in my larger surname group a Co-Admin who has ONLY Ancestry Y 33 markers and 23andme SNPS for her now deceased husband and brother so I am trying to help..the $19 transfer will not allow matches.

                          So please direct me to the BEST directions you have for the 23andme to Y Snps..
                          Thank you for all your efforts Felix..I hope to begin to figure this out so that I then CAN help my BIG Y group testers and also compare the 23andme snps against those results.

                          "When the tide rises all the boats float" is my motto about helping others and you surely do that!

                          Comment


                          • #14
                            Originally posted by Kathleen Carrow View Post
                            Hi Felix
                            You were kind enough to do my grandson's for me.. I also have in my larger surname group a Co-Admin who has ONLY Ancestry Y 33 markers and 23andme SNPS for her now deceased husband and brother so I am trying to help..the $19 transfer will not allow matches.

                            So please direct me to the BEST directions you have for the 23andme to Y Snps..
                            Your co-admin can go to the Haplogroup Tree Mutation Mapper at 23andMe to see the list of derived SNPs:

                            https://www.23andme.com/you/labs/hap...ee_mut_mapper/

                            Comment


                            • #15
                              Originally posted by Ann Turner View Post
                              Your co-admin can go to the Haplogroup Tree Mutation Mapper at 23andMe to see the list of derived SNPs:

                              https://www.23andme.com/you/labs/hap...ee_mut_mapper/
                              Ann,
                              Thank you so much for that..isn't it just the terminal snps that are seen there?
                              Some people argue that the terminal snps at 23andme, which in this case are U209,P277 and P278 do not indicate that the ones that preceded it were negative. Up stream I think it is?

                              In another case I have had a haplogroup admin say that my L52,P311,L11,P310 ancestral line's results from 23andme do not mean anything and that more snps should be tested. To be that seems counterproductive but perhaps I am incorrect?
                              Last edited by Kathleen Carrow; 10 April 2014, 06:21 PM.

                              Comment

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