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

# cnvkit-breaks(1)

List the targeted genes in which a copy number breakpoint occurs.

## NAME

cnvkit\_breaks - List the targeted genes in which a copy number breakpoint occurs.

## DESCRIPTION

usage: cnvkit.py breaks \[-h\] \[-m MIN\_PROBES\] \[-o FILENAME\] filename segment

### positional arguments:

- filename

  Processed sample coverage data file (\*.cnr), the output of the 'fix' sub-command.

- segment

  Segmentation calls (.cns), the output of the 'segment' command).

### options:

- **-h**, **--help**

  show this help message and exit

- **-m** MIN\_PROBES, **--min-probes** MIN\_PROBES

  Minimum number of within-gene probes on both sides of a breakpoint to report it. \[Default: 1\]

- **-o** FILENAME, **--output** FILENAME

  Output table file name.