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finding Big-Y unnamed variants shared with matches

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  • finding Big-Y unnamed variants shared with matches

    I received my fathers Big-Y results yesterday and there are 13 matches and 14 unnamed variants, Haplogroup is R-Y1392 (equivalent to R-Y2902 at YFull).

    Of all matches, 5 are in the same Haplogroup as me and the rest in downstream Haplogroups.

    For each match I'd like to find out if there are shared unnamed variants with my father's results and which they are. This is a simple and obvious question, but I only found a complicated and error-prone way to do it:

    For each match I checked which of my (really my father's but for simplicity I say my) unnamed variants would be in the "Non-Matching Variants"-box for the match. If they are not there, the match could have a no-call in that position or we could have a shared unamed variant. To find out, I open the "Shared Variants"-box for the match and look up the position (Navigation in this box is annoying, mainly since there's no possibility to filter for the position name and there are > 300000 entries...). When I don't find the position there, it must mean that this was a no-call for the position; if it's there, then we have a shared unnamed variant.

    Is the described method a feasible way to find shared unnamed variants for matches? Is there a simpler way to do it? (there *must* be!).

    For one match, I found three shared unnamed variants. There are still 27 Non-Matching Variants listed, birth place of ancestors is 1.400km apart, and the surnames match only on the first letter - most likely transscription from Cyrillic alphabet by the match . But I guess these variants would be good for a sub-branch in the BigY Tree or YFull Tree.

  • #2
    Originally posted by chr View Post
    I received my fathers Big-Y results yesterday and there are 13 matches and 14 unnamed variants, Haplogroup is R-Y1392 (equivalent to R-Y2902 at YFull).

    Of all matches, 5 are in the same Haplogroup as me and the rest in downstream Haplogroups.

    For each match I'd like to find out if there are shared unnamed variants with my father's results and which they are. This is a simple and obvious question, but I only found a complicated and error-prone way to do it:

    ... Is there a simpler way to do it? (there *must* be!).
    There is no sure way at all without obtaining the VCF and BED files (or the nonexistant BAM file) for all people to be compared. The data on the web pages is insufficient.

    A sufficient reason for saying this is that FTDNA uses an arbitrary cutoff in the number of "reads" for determining a "call". And it is impossible to find out the number of reads on the web pages if the no-call is an unnamed variant.

    One must also check to see if the region of the marker is a bad one.

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    • #3
      Originally posted by dtvmcdonald View Post
      There is no sure way at all without obtaining the VCF and BED files (or the nonexistant BAM file) for all people to be compared. The data on the web pages is insufficient.

      A sufficient reason for saying this is that FTDNA uses an arbitrary cutoff in the number of "reads" for determining a "call". And it is impossible to find out the number of reads on the web pages if the no-call is an unnamed variant.
      Do I understand you right that you are refering to "unknown-confidence" calls, who are equivalent to no-calls in terms of matching and visibility?

      It looks to me there used to be a "Confidence" Display/Sort column in the "Named Variants", "Unnamed Variants" and "Shared Variants" browsing windows. They don't show for me (tested in Firefox and Chrome - so FTDNA removed it, right?), but they are described and shown in the FTDNA Learning Center and in Roberta Estes Big-Y HG38 article of january.

      Originally posted by dtvmcdonald View Post
      One must also check to see if the region of the marker is a bad one.
      Thanks for pointing that out. One of my unnamed variants seems to be in "synthetic assembled centromeric region (CEN)" and another in "DYZ19 125 bp repeat region" (ranges and names taken from yseq "Wish a SNP" Info. So I guess I can ignore these.

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      • #4
        Originally posted by chr View Post

        Thanks for pointing that out. One of my unnamed variants seems to be in "synthetic assembled centromeric region (CEN)" and another in "DYZ19 125 bp repeat region" (ranges and names taken from yseq "Wish a SNP" Info. So I guess I can ignore these.
        That's the default action. However, there are lots of SNPs inside the DYZ19 region that have proven to be completely reliable using BigY or other Illumina sequenced tests. MAny of these cannot be tested by Sanger sequencing or the method used by the FTDNA SNP Packs. In my project we have three of these that are very important.

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