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SNP disappeared with update of BigY

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  • SNP disappeared with update of BigY

    An SNP that was an important link between two branches in my project disappeared after the BigY update:

    BY6658 13715897 (hg19) 11560221 (hg38)

    Can anyone explain why it disappeared and is it possible to get it back. Out of five four BigYs that were taken before the update, two were positive as novel variants. I was able to get it named and now it is gone. It was an important subclade as this is a multisurname project.

    Michael Talley

  • #2
    Which test(s) had been used to determine this SNP?


    • #3
      Could you post the entries for that SNP in the VCF files
      if they are there? What do the BED files look like at that location and vicinity?

      Does that SNP show up in the chromosome browser? None
      of my files show it.


      • #4
        Wait for the BAM

        When one remaps sequences against a new reference not all of the sequences may get mapped to back to the "same" location. Changes in the new reference sequence will drive how the sequence fragments are mapped. The vast majority in the good regions will get mapped correctly but the presence of the new/updated regions may siphon away enough fragments to lower the coverage/quality in a region to a point where a positive call is no longer made. You should wait for the BAM files and look at all of the expected positive calls and a couple of the known negatives to see if there is sufficient evidence to support a positive call under the new mapping.

        Of course results from individual SNP testing can also support the presence of the level.