NAME

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

DESCRIPTION

       usage: cnvkit coverage [-h] [-f FILENAME] [-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

       -f FILENAME, --fasta FILENAME
              Reference genome, FASTA format (e.g. UCSC hg19.fa)

       -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]