table of contents
| CNVKIT_FIX(1) | User Commands | CNVKIT_FIX(1) |
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 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).
optional arguments:¶
- -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.
| October 2021 | cnvkit fix 0.9.9 |