When viewing a BAM, can you specify regions of a certain coverage?

[oiiio]

Does anyone know of a tool to view only regions of a BAM with specific coverage? Ideally, it would constrain the coverage using either a max or min

[swbarnes2]

You could make a pileup, which would have the depth at every point. Then some kind of script to make a .bed file of all those windows you wanted, and you can apply the .bed file to the .bam with samtools view to get a .bam just at those coordinates.

You could probably use BEDTools to do much of that. I'm not sure there's an easier way.

[Jim Robinson]

Elaborating on this just a little... After creating the bed you can load both the bed and the BAM into IGV. Then click on the name panel over the bed track, and use ctrl-f to skip from one region to the next.

[mgogol]

I think you could use genomeCoverageBed from bedtools for the first step. I know you could do the second part in R quite easily, but it would take me awhile to figure that one out. Once you have a bed file you could use intersectBed to get a bam just with those coords.