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  • Cutting bases from reads in a bam file - what other fields need to be changed?

    Hi,

    I'm writing a tool, which needs to cut bases from reads in a bam file. I'm not to familiar with the exact specifications of the bam format. So I'd like to ask what information I may to change to keep the bam correct.

    What I found so far:
    1. the qualities
    2. the CIGAR string
    3. the mate position, if bases from the start of mate were cut

    Anything else?

  • #2
    Probably all of the OPT flags (field 12). Official specifications are at:

    Comment


    • #3
      Trimming can also affect the mapping quality, and the bit flag might be incorrect if the shorter read becomes a multi-mapper. And, short of realignment, it will not be trivial to correct those values. That's why trimming is performed on FASTQs rather than BAMs.

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