text: user16204: I am using bedtools to caculate the coverage of my targets of my WES data, to later plot. But to plot, I need to know what to plot and what it is I am seeing. I have unsuccefully tried to find what exactly the columns are in the output of the bedtool coverage, and how to read them. Also, the documentation does not help me a lot, and I find it confusing. Does anyone know, or where to find this a bit more elaboratly explained?
  I used the following code:
  bedtools coverage -hist -abam input.bam -b input.bed > output >2 log
  Correction note: the code above is actually wrong (thanks to @Alexlok) and should be:
  bedtools coverage -hist -a input.bed -b input.bam > output 2> log
  And the output is (first line):
  
  Last 5 lines:
  
  Thank you in advance
  
  user16204: Found it, it is an extended .bed file format, so not specific to bedtools output: source bed file output.
  With 4 added columns to the end from bedtools -hist option:
  bedtools -hist option
  
original_text: 16204: <p>I am using <a href="https://bedtools.readthedocs.io/en/latest/index.html#" rel="nofollow noreferrer">bedtools</a> to caculate the coverage of my targets of my WES data, to later plot. But to plot, I need to know what to plot and what it is I am seeing. I have unsuccefully tried to find what exactly the columns are in the output of the <a href="https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html#" rel="nofollow noreferrer">bedtool coverage</a>, and how to read them. Also, the documentation does not help me a lot, and I find it confusing. Does anyone know, or where to find this a bit more elaboratly explained?</p>
  <p>I used the following code:</p>
  <p><code>bedtools coverage -hist -abam input.bam -b input.bed &gt; output &gt;2 log</code></p>
  <p><strong>Correction note</strong>: the code above is actually wrong (thanks to @Alexlok) and should be:
  <code>bedtools coverage -hist -a input.bed -b input.bam &gt; output 2&gt; log</code></p>
  <p>And the output is (first line):</p>
  <p><a href="https://i.stack.imgur.com/M2fdP.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/M2fdP.png" alt="First 5 lines" /></a></p>
  <p>Last 5 lines:</p>
  <p><a href="https://i.stack.imgur.com/008DK.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/008DK.png" alt="Last 5 Lines" /></a></p>
  <p>Thank you in advance</p>
   16204: <p>Found it, it is an extended .bed file format, so not specific to bedtools output: <a href="http://www.ensembl.org/info/website/upload/bed.html#optional" rel="nofollow noreferrer">source bed file output</a>.
  With 4 added columns to the end from bedtools -hist option:
  <a href="https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html" rel="nofollow noreferrer">bedtools -hist option</a></p>
  