DOKK / manpages / debian 10 / cnvkit / cnvkit-fix.1.en
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] [--no-gc] [--no-edge] [--no-rmask] [-i SAMPLE_ID]

[-o FILENAME] target antitarget reference

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

show this help message and exit
Skip GC correction.
Skip edge-effect correction.
Skip RepeatMasker correction.
Sample ID for target/antitarget files. Otherwise inferred from file names.
Output file name.
March 2019 cnvkit_fix 0.9.5