Question: Depth of Coverage - Calculated Per Probe / Bed Region
gravatar for jnowacki
2.1 years ago by
jnowacki70 wrote:

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

depth tool bam bed • 3.7k views
ADD COMMENTlink modified 2.1 years ago by Kevin Blighe55k • written 2.1 years ago by jnowacki70
gravatar for Kevin Blighe
2.1 years ago by
Kevin Blighe55k
Kevin Blighe55k wrote:

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


ADD COMMENTlink written 2.1 years ago by Kevin Blighe55k
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