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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.

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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
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    $\begingroup$ Are you sure that those statistics are the ones that make the most sense for RNASeq? $\endgroup$
    – swbarnes2
    Mar 22 at 16:15
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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.

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