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

[Flo1000]

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?

[westerman]

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

https://samtools.github.io/hts-specs/SAMv1.pdf

[HESmith]

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.