text: user10383: 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.
  
  user3360: You could use samtools coverage as explained in the manual 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
  
  
original_text: 10383: <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>
   3360: <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>
  