Man page - cnvkit-fix(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_FIX
NAMEDESCRIPTION
positional arguments:
options:
NAME
cnvkit_fix - Combine target and antitarget coverages and correct for biases.
Adjust raw
coverage data according to the given reference, correct
potential
biases and re-center.
DESCRIPTION
usage: cnvkit.py
fix [-h] [-c] [-i SAMPLE_ID] [--no-gc] [--no-edge]
[--no-rmask] [-o FILENAME]
target antitarget reference
positional arguments:
|
target |
Target coverage file (.targetcoverage.cnn). |
antitarget
Antitarget coverage file (.antitargetcoverage.cnn).
reference
Reference coverage (.cnn).
options:
-h , --help
show this help message and exit
-c , --cluster
Compare and use cluster-specific values present in the reference profile. (Requires that the reference profile was built with the --cluster option.)
-i SAMPLE_ID, --sample-id SAMPLE_ID
Sample ID for target/antitarget files. Otherwise inferred from file names.
--no-gc
Skip GC correction.
--no-edge
Skip edge-effect correction.
--no-rmask
Skip RepeatMasker correction.
-o FILENAME, --output FILENAME
Output file name.