Number of sequenced positions from a BAM file

Question

[rubic]

Hi,

Is there a samtools or other tool command that given a bam (and/or indexed bam) file will report the number of sites sequenced?

Answer 1

[Devon Ryan]

I'm sure there are a few out there (there's probably something in picard), but it's simple enough to pipe samtools depth through awk and just quickly count things. This has the benefit of allowing you to easily filter by MAPQ and other things.