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| CNVKIT_COVERAGE(1) |
User Commands |
CNVKIT_COVERAGE(1) |
NAME¶
cnvkit_coverage - Calculate coverage in the given regions from BAM read depths.
DESCRIPTION¶
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]
