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Big Y - YFull - Y-Chr Sequence Interpretation Service

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  • #16
    I was looking at STR coverage and it looks like there is
    data there that is not in the bed file. However, I have
    no matching bed and bam files, it just a general
    look. It will take a careful look an many bam files to
    see what the coverage usually is.

    Comment


    • #17
      Originally posted by Rebekah Canada View Post
      Hi,

      Please be aware that your BAM file is highly personal genomic data. It is Y-Chromosome, a smidgen of autosomal, and enough mtDNA to make a good guess at your deep clade.

      Mind you, it is not the 200X NextGen mtDNA sequencing we do for our mtDNA product.

      However, it is enough information that someone could make a really good educated guess at the file belonging to you or your brother. Do you remember when 23andMe first launched and we all figured out who their example profiles really were within days?
      I think there's a decent chance that the mtDNA coverage in the BAM file would be detailed enough to include "private" SNPs (i.e. not used to define a subclade)as well as mutations associated with medical conditions.

      What genes (if any) are included in the regions covered by the Big Y? Would infertility problems be evident, for example? We know that that routine Y-DNA testing can reveal a large-scale deletion including genes involved in spermatogenesis, when people get nulls for certain markers such as DYS464.

      http://omim.org/entry/415000

      But aside from that, I'm not aware of any special concerns. OMIM (Online Mendelian Inheritance in Man)lists some phenotypes linked to Y genes. But some of those are very shaky associations, like this one based on a small pedigree:

      http://omim.org/entry/400004

      People can check the box for chromosome Y in this query screen if they want to explore other records:

      http://omim.org/search/advanced/

      Comment


      • #18
        Originally posted by Ann Turner View Post
        I think there's a decent chance that the mtDNA coverage in the BAM file would be detailed enough to include "private" SNPs (i.e. not used to define a subclade)as well as mutations associated with medical conditions.

        http://omim.org/search/advanced/
        It absolutely certainly is that good. It's not 100%
        in either of the files I looked at but at most a
        dozen bases were not tested at all. Most had 50+ coverage,
        some huge coverage.

        Of course, you can use samtools to chop out only the Y
        part if you want to share only that.

        Comment


        • #19
          Originally posted by dtvmcdonald View Post
          Of course, you can use samtools to chop out only the Y part if you want to share only that.
          YFull's web site says: "MtDNA (rCRS and RSRS) optionally". This sounds like they specifically offer the choice of ignoring your mtDNA data, if you prefer that.

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          • #20
            Originally posted by MitchellSince1893 View Post
            Just requested my BAM file. How long did you all have to wait before available from FTDNA?

            Also, how were you notified that they were ready?
            Just got the notification that my bam file is available and 5 mins later I ordered the Y-Full analysis. WooHoo!

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            • #21
              Getting This message when I send to Y-full

              Tried to send my BigY results link to Yfull a couple of times using different emails but I keep getting this message

              This is the mail system at host mail.semargl.me.

              I'm sorry to have to inform you that your message could not
              be delivered to one or more recipients. It's attached below.

              For further assistance, please send mail to postmaster.

              If you do so, please include this problem report. You can
              delete your own text from the attached returned message.
              Both times I did get a "Thank you for your order" but I'm not sure if it's getting through to Y full. Does anyone know how can verify whether they actually got the message?

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              • #22
                Originally posted by MitchellSince1893 View Post
                Tried to send my BigY results link to Yfull a couple of times using different emails but I keep getting this message



                Both times I did get a "Thank you for your order" but I'm not sure if it's getting through to Y full. Does anyone know how can verify whether they actually got the message?
                This is the email address that I used to communicate: [email protected].

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                • #23
                  thanks. I tried entering a 3rd email address and so far so good...no return error messages.

                  Comment


                  • #24
                    Originally posted by MitchellSince1893 View Post
                    Just got the notification that my bam file is available and 5 mins later I ordered the Y-Full analysis. WooHoo!
                    Congrats!Thanks for the info!just checked my email,also got my link today.requested on 3/19/14.

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                    • #25
                      What are the cons?

                      So I understand the pros to submitting your BAM-file to Yfull for analysis. What are possible cons? Just want to make an informed decision.

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                      • #26
                        Well, all your laundry is out there, so to speak, and there's no putting it back in the hamper.

                        It's supposedly anonymous, of course, but somewhere in their system, your data will be linked with your name...

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                        • #27
                          Originally posted by Varego View Post
                          Well, all your laundry is out there, so to speak, and there's no putting it back in the hamper.

                          It's supposedly anonymous, of course, but somewhere in their system, your data will be linked with your name...
                          Ok, I get that. And how can that potentially become a problem for someone? What can be read from the data that might pose a danger in any way even when linked to one´s name? Not even advanced identity thieves can utilize that kind of information, can they? Is it likely that future technologies will make it possible to use the data in unforeseen ways?

                          Comment


                          • #28
                            Originally posted by Inge View Post
                            Ok, I get that. And how can that potentially become a problem for someone? What can be read from the data that might pose a danger in any way even when linked to one´s name? Not even advanced identity thieves can utilize that kind of information, can they? Is it likely that future technologies will make it possible to use the data in unforeseen ways?
                            Yeah, I've been thinking about the same thing. I'm generally a privacy conscious person, but my DNA results & name are already tied together via 111 Y-STR markers and public/known SNPs on FTDNA's public projects pages. What else would I be giving away?

                            Comment


                            • #29
                              Originally posted by KSDA View Post
                              Yeah, I've been thinking about the same thing. I'm generally a privacy conscious person, but my DNA results & name are already tied together via 111 Y-STR markers and public/known SNPs on FTDNA's public projects pages. What else would I be giving away?
                              This, perhaps. I haven't played with the SNPTips, as I'm traveling with only my iPad, but I plan to when I get home...

                              Comment


                              • #30
                                Got confirmation email that Yfull got my link. Also sent it to FGC as well.

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