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Big Y enhancements started Oct 10th

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  • HG19 vs HG38 genome and SNP refinement.

    Can someone explain the difference in results by switching from HG19 to HG38 genomes? I know that a few of us have seen elimination of prior positive SNPs and also addition of many negative SNP's and some new positive SNPs as well. Some who have had the eliminated positive SNPs tested at yseq report they are still positive there.

    Also is there anyway to tell who has been re-worked under HG38 vs HG19. Seems like it would be apples to oranges comparisons if some have reprocessed and others in a given project haven't.

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    • hg38 conversion

      How many of you are still waiting on an old Big Y test conversion from hg 19 to hg 38?

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      • I'm still waiting for my father's conversion from an old Big Y test.

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        • I'm still waiting on several conversions. After much prodding, I was informed that the lab analysis itself is being redone.

          As to telling if the conversion is done: go to the person's BigY web page. If the page works, even if there are no matches, its done. If its not done, it won't work. There's
          nothing there.

          BAM files may still be there. If so, they are the old ones,
          at least so far.

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          • Three of my project's BigY converts are still outstanding.
            I'm told the lab work itself is being rerun.

            But I wonder what happens if it CAN'T be rerun.

            The usual reason for this is that the sample on hand is exhausted and the testee dead.

            Will even one of these this prevent the conversion from ever being finished, and hence, we never get converted B38 BAM files?

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            • Originally posted by dtvmcdonald View Post
              Three of my project's BigY converts are still outstanding.
              I'm told the lab work itself is being rerun.

              But I wonder what happens if it CAN'T be rerun.

              The usual reason for this is that the sample on hand is exhausted and the testee dead.


              Will even one of these this prevent the conversion from ever being finished, and hence, we never get converted B38 BAM files?
              This is very concerning.

              This scenario had to be unexpected by FTDNA?

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              • Still Waiting

                I know of 8 BY kits from 2014 and 2015 in one of my projects that still have upgrades in process. I finally opened a request and FTDNA is supposedly looking into it for an answer.

                Also still waiting on my dad's BY kit results from August. I checked before ordering to make sure there was plenty of dna on file and was assured it was fine. Hope that still holds. Batch 781. It seems there are still several BY from that batch still pending based on posts in the BigY group on Facebook.

                Angelia

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                • Originally posted by Eric McGregor View Post
                  Also is there anyway to tell who has been re-worked under HG38 vs HG19. Seems like it would be apples to oranges comparisons if some have reprocessed and others in a given project haven't.

                  If you are a project admin, just look to see if a person's web page has data. If so, its build 38.


                  They are now taking BAM file requests. They are not promising that they are actually being processed, but are promising they will be some day.

                  As to a mix of 37 (19) and 38 files .... well, just converting a bed/vcf pair from a 37 to a 38 by redoing all the positions works fine. Of course, you don't get all
                  the new build 38 file info. If a position in a build 37 file fails to convert, except in the rarest of cases it is garbage data and you just forget it. I've converted hundreds of files and can count on the fingers of one hand the numbers of real, useful SNPs affected by other than one problem. That problem is that the number of "reads" crosses their "quality control borderline" .. which can happen either way. In ALL cases a careful examination of the Build 37 BAM and the Build 38 VCF shows that the build that generated data was correct. This of course will, eventually, be a wrong statement, but it will be a very very rare event.

                  Edit: I'm talking real SNPs here, not garbage. Anything above position 50,000,000
                  is garbage as far as I can see.
                  Last edited by dtvmcdonald; 3rd February 2018, 02:07 PM.

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                  • BigY Still Waiting

                    I upgraded dad 's kit to BigY when the sale was on, it has now been pushed back to April
                    My rerun November 2017 results have me with no matches I am still R-BY3554
                    How long before they fix whatever they are doing

                    Colin

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