DOKK / manpages / debian 10 / cnvkit / cnvkit-coverage.1.en

cnvkit_coverage - Calculate coverage in the given regions from BAM read depths.

usage: cnvkit coverage [-h] [-c] [-q MIN_MAPQ] [-o FILENAME] [-p [PROCESSES]]

bam_file interval

Mapped sequence reads (.bam)
Intervals (.bed or .list)

show this help message and exit
Get read depths by counting read midpoints within each bin. (An alternative algorithm).
Minimum mapping quality score (phred scale 0-60) to count a read for coverage depth. [Default: 0]
Output file name.
Number of subprocesses to calculate coverage in parallel. Without an argument, use the maximum number of available CPUs. [Default: use 1 process]
March 2019 cnvkit_coverage 0.9.5