CNVKIT_COVERAGE

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)

options:

-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]