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CNVKIT_FIX(1) User Commands CNVKIT_FIX(1)


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.


usage: cnvkit fix [-h] [-c] [-i SAMPLE_ID] [--no-gc] [--no-edge] [--no-rmask]

[-o FILENAME] target antitarget reference

positional arguments:

Target coverage file (.targetcoverage.cnn).
Antitarget coverage file (.antitargetcoverage.cnn).
Reference coverage (.cnn).


show this help message and exit
Compare and use cluster-specific values present in the reference profile. (Requires that the reference profile was built with the --cluster option.)
Sample ID for target/antitarget files. Otherwise inferred from file names.
Skip GC correction.
Skip edge-effect correction.
Skip RepeatMasker correction.
Output file name.
September 2022 cnvkit fix 0.9.9