Identify and count gaps in sam/bam files

Question

[shpak.max]

Is there a straightforward way to identify and tally the gaps in a sam/bam file created by bwa? A glance at the mapping using IGV suggests that there are virtually no gaps in a mapping that I recently generated, which is problematic. I would like to know if there are any gaps at all.

Is there some way to doing this using a samtools function, or perhaps some other application?

[WouterDeCoster]

And with gap, you mean a portion of the genome that has no aligned reads?

[shpak.max]

I'm referring to gaps corresponding to indels.

[Mark]

You need to do variant calling.

[Mark]

samtools depth -aa should do what you're after. It outputs a tab de limited file. Then use your favorite tool to compute visualize.