Man page - cnvkit-coverage(1)
Packages contains this manual
- cnvkit-import-theta(1)
- cnvkit-coverage(1)
- cnvkit-metrics(1)
- cnvkit-import-seg(1)
- cnvkit-export(1)
- cnvkit-breaks(1)
- cnvkit-fix(1)
- cnvkit-segmetrics(1)
- cnvkit-batch(1)
- cnvkit-import-rna(1)
- cnvkit-bintest(1)
- cnvkit-diagram(1)
- cnvkit-call(1)
- cnvkit-autobin(1)
- cnvkit-access(1)
- cnvkit-antitarget(1)
- cnvkit-sex(1)
- cnvkit-segment(1)
- cnvkit-genemetrics(1)
- cnvkit-heatmap(1)
- cnvkit-target(1)
- cnvkit-import-picard(1)
- cnvkit-reference(1)
- cnvkit-scatter(1)
apt-get install cnvkit
Manual
CNVKIT_COVERAGE
NAMEDESCRIPTION
positional arguments:
options:
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]
[-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]