Getting coordinates with bad deep/coverage from a bam file

Question

[Enka]

I received .bam files for bacterial genomes sequenced by SOLiD and mapped to a reference genome by bioscope. I have found that some areas have really few reads aligned (as few as 2). I would like to know if there is a way to get the coordinates of the regions that have a deep (or coverage) below certain threeshold, so I can assess how big is this problem for each aligment.

Answer 1

[GouthamAtla]

A: How get intervals of low coverage from a genome sequence?

[Enka]

My bad. Thanks a lot.