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

# cnvkit-bintest(1)

Test for single-bin copy number alterations.

## NAME

cnvkit\_bintest - Test for single-bin copy number alterations.

## DESCRIPTION

usage: cnvkit.py bintest \[-h\] \[-s FILENAME\] \[-a ALPHA\] \[-t\] \[-o OUTPUT\]

-

  cnarray

### positional arguments:

- cnarray

  Bin-level log2 ratios (.cnr file), as produced by 'fix'.

### options:

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

  show this help message and exit

- **-s** FILENAME, **--segment** FILENAME

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

- **-a** ALPHA, **--alpha** ALPHA

  Significance threhold. \[Default: 0.005\]

- **-t**, **--target**

  Test target bins only; ignore off-target bins.

- **-o** OUTPUT, **--output** OUTPUT

  Output filename.