Depth of Coverage - Calculated Per Probe / Bed Region

Question

[jnowacki]

I'm trying to find out the average depth of coverage per target region in a bed file. I can easily use bedtools -depth to find the depth of coverage at each base, but I'd much rather have it as average coverage per region. The bedtools -hist option produces 110 reports on one of my features. I only want 1 number (average coverage) per target region. Any way to do this?

I found threads from a few years ago but wonder if there is anything current. One of the solutions doesn't compile on my Ubuntu server and the bash script gets a "fatal: division by zero attempted"

Depth of coverage for specific target from bam file

Answer 1

[Kevin Blighe]

Please take a look at my answer here: Compute mean depth coverage for exome data with paired end, overlapping, features I believe that you require BEDTools version > 2.0.

Also some simple code for plotting the profile: Histogram showing overlap between 2 bed files

Kevin