Answers.Body: <p>You could use <code>samtools coverage</code> as explained in the <a href="http://www.htslib.org/doc/samtools-coverage.html" rel="nofollow noreferrer">manual</a> of samtoools.</p>
  <p>Here is a example which is also described on the manual site.</p>
  <pre><code>samtools coverage -r chr1:1M-12M input.bam
  
  #rname  startpos  endpos    numreads  covbases  coverage  meandepth  meanbaseq  meanmapq
  chr1    1000000   12000000  528695    1069995   9.72723   3.50281    34.4       55.8
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-22T16:15:24.913Z
Answers.Text: Are you sure that those statistics are the ones that make the most sense for RNASeq?
Answers.UserDisplayName: swbarnes2
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Answers.CreationDate: 2021-03-21T19:23:10.480Z
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Answers.LastEditDate: 2021-03-22T19:01:19.597Z
Answers.UserDisplayName: Mr_Z
Answers.Body: <p>I've used <a href="https://genome.sph.umich.edu/wiki/BamUtil" rel="nofollow noreferrer">https://genome.sph.umich.edu/wiki/BamUtil</a> before. I think this has all the functionality you want and the Devs are responsive which is nice.</p>
  
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Answers.CreationDate: 2021-03-21T03:45:49.677Z
Answers.LastActivityDate: 2021-03-21T03:45:49.677Z
Answers.UserDisplayName: Liam McIntyre
Body: <p>I have a .bam alignment file and a genome reference .fasta file. I am looking for a easy to use tool (that I can reference in a publication) to calculate the percentage coverage of the reference by the alignment and if possible also: average depth of reads that cover the gene, min/max depths. Running plot would be nice but not essential.</p>
  <p>I wrote some python code to calculate coverage percent, but I want to reference the tool I use in a paper and dont want to mess with making a git repo and linking to it in the paper just for this simple analysis.</p>
  
Tags: <rna-seq><phylogenetics>
Title: Calculate genome coverage and depth from alignment
ThreadText: # Calculate genome coverage and depth from alignment
  
  (Asked by: username_0 on 2021-03-20)
  
  I have a .bam alignment file and a genome reference .fasta file. I am looking for a easy to use tool (that I can reference in a publication) to calculate the percentage coverage of the reference by the alignment and if possible also: average depth of reads that cover the gene, min/max depths. Running plot would be nice but not essential.
  
  I wrote some python code to calculate coverage percent, but I want to reference the tool I use in a paper and dont want to mess with making a git repo and linking to it in the paper just for this simple analysis.
  
  **Tags:** rna-seq, phylogenetics
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2021-03-21. Score: 2
  
  You could use `samtools coverage` as explained in the [manual](http://www.htslib.org/doc/samtools-coverage.html) of samtoools.
  
  Here is a example which is also described on the manual site.
  
  ```
  samtools coverage -r chr1:1M-12M input.bam
  
  #rname  startpos  endpos    numreads  covbases  coverage  meandepth  meanbaseq  meanmapq
  chr1    1000000   12000000  528695    1069995   9.72723   3.50281    34.4       55.8
  
  ```
  
  > **Comments:**
  > **username_2**: Are you sure that those statistics are the ones that make the most sense for RNASeq?  
  
  ---
  
  ### Answer by username_3 on 2021-03-21. Score: 0
  
  I've used <https://genome.sph.umich.edu/wiki/BamUtil> before. I think this has all the functionality you want and the Devs are responsive which is nice.
  
  
  ---
  
  