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Old 10-29-2013, 01:48 PM   #3
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 824
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I would use bedtools (which can use BAM files as input). Use genomecov to get the coverage all across the genome:

http://bedtools.readthedocs.org/en/l...genomecov.html

Or just coverage if you have a specific gff/bed file with the region that you want to determine the coverage for:

http://bedtools.readthedocs.org/en/l.../coverage.html

edit: sorry, that's just for the base-pair coverage (independent of the base). I suspect that per-nucleotide counts in a particular region is straying into "needs a custom script to work it out from the samtools mpileup output" territory.

Last edited by gringer; 10-29-2013 at 01:53 PM.
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