NAME

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

DESCRIPTION

usage: cnvkit.py coverage [-h] [-f FILENAME] [-c] [-q MIN_MAPQ] [-o FILENAME]

-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]