---
name: "cnvkit-fix"
section: "1"
platform: "linux"
package: "cnvkit"
version: "0.9.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cnvkit-fix"
---

# cnvkit-fix(1)

Combine target and antitarget coverages and correct for biases. Adjust raw coverage data according to the given reference, correct potential biases and re-center.

## 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.