Obtain coordinates of insert (e.g. bed file) from aligned paired-end reads (sam file)

[jajclement]

Hi,

I am just trying to obtain start and end coordinates of the insert (something like a bed file) from my alignment file (.sam) of paired-end reads (that is to reconstruct the fragment information in one lign from the information of both aligned mates stored in two ligns in the sam file)
I aligned my paired-end reads with bowtie2 and only retained paired reads aligning only one time.
I am looking for a tool doing this but was unable to found something that already exists.

Does anyone have an idea for doing this?

Thanks for your advices!