Is your feature request related to a problem? Please specify.

I'd like a simple way to calculate the coverage stats for a bam file. The closest out-of-the-box thing I can find is samtools coverage. I run the command like so:

samtools coverage input.bam

The simple summary stats are great, and what I need, except for the fact that the 'covbases' statistic is defined as 'Number of covered bases with depth >= 1'. Instead, I would prefer to have the statistic of 'Number of covered bases with depth >= X', where X is a minimum depth defined by a command line flag.

Describe the solution you would like.

I would like to be able to use a command like:

samtools coverage --min-depth 20 input.bam

With the output statistics being calculated (in this case) only for bases covered with depth >=20. Would this be possible? So far I use a different command like:

bedtools genomecov -ibam input.bam -d | awk '$3 >= 20 { count++ } END { print (count/NR)*100 }'

But I'd prefer to have the much simpler samtools command and simplify the dependencies of my pipeline.

Would this be possible? Thanks!