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.py fix [-h] [-c] [-i SAMPLE_ID] [--no-gc] [--no-edge]

[--no-rmask] [-o FILENAME]
target antitarget reference

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.
July 2023 cnvkit.py fix 0.9.10