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.