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?
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?
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