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DF27 missing from my BAM file

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  • DF27 missing from my BAM file

    I am ZZ20-1. i have tested positive for DF27. I did the BigY and downloaded my BAM file. DF27 is a no show. How can that be?

  • #2
    Someone in the R-DF27 project (which you might consider joining) said the following about that:
    To get it called, one usually needs two consecutive "nested" runs of Sanger sequencing (to determine whether it's present on the forward or the back strand, I think); and the BigY test uses a different technology. It sees vastly more pieces of your Y chromosome than a Sanger test, but in little chunks; then they have to be stitched back together by the computer, and it isn't a very subtle technique. Especially near the boundaries between chunks. Or on sections of the Y that look just like sections of the X chromosome (which isn't where YDNA SNPs happen). So, BigY doesn't necessarily get unambiguous reads, of things that were inherently hard to read in the first place. For many people, a DF27+ can be teased out of the BigY BAM file. But if you already have an unambiguous call for something already known to be downstream of DF27 -- why bother?