Provided by: cnvkit_0.9.6-3_amd64
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 positional arguments: bam_file Mapped sequence reads (.bam) interval Intervals (.bed or .list) optional arguments: -h, --help show this help message and exit -c, --count Get read depths by counting read midpoints within each bin. (An alternative algorithm). -q MIN_MAPQ, --min-mapq MIN_MAPQ Minimum mapping quality score (phred scale 0-60) to count a read for coverage depth. [Default: 0] -o FILENAME, --output FILENAME Output file name. -p [PROCESSES], --processes [PROCESSES] Number of subprocesses to calculate coverage in parallel. Without an argument, use the maximum number of available CPUs. [Default: use 1 process]