paired reads aligned at the same genomic position

Question

[irfanwustl]

We know sometimes paired reads can align at the same position. In such a case, is there any simple command to remove one of the paired reads from the bam file?

Answer 1

[MatthewP]

Paired reads align at same position probably because some insert fragments is too short that even shorter than your reads, you can use fastp to get fragment length distribution report, so you can see is there some fragments too short.
I don't think you need to remove one of them, you can see bowtie2 manual "dovetail" part, aligner can handle such case.

[irfanwustl]

Actually, I want to count how many reads aligned to a specific position (like depth) from a python code. That's why I was trying to remove one read.