table of contents
| 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] [-f FILENAME] [-c] [-q MIN_MAPQ] [-o FILENAME]
- [-p [PROCESSES]]
- bam_file interval
positional arguments:¶
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]
| October 2021 | cnvkit coverage 0.9.9 |