---
name: "cnvkit"
section: "1"
platform: "linux"
package: "cnvkit"
version: "0.9.9-2+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/cnvkit"
---

# cnvkit(1)

a command-line toolkit for copy number analysis.

## NAME

cnvkit - a command-line toolkit for copy number analysis.

## DESCRIPTION

usage: cnvkit \[-h\]

-

  {batch,target,access,antitarget,autobin,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,genemetrics,gainloss,sex,gender,metrics,segmetrics,bintest,import-picard,import-seg,import-theta,import-rna,export,version} ...

CNVkit, a command-line toolkit for copy number analysis.

### positional arguments:

- {batch,target,access,antitarget,autobin,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,genemetrics,gainloss,sex,gender,metrics,segmetrics,bintest,import-picard,import-seg,import-theta,import-rna,export,version}

  Sub-commands (use with **-h** for more info)

- batch

  Run the complete CNVkit pipeline on one or more BAM files.

- target

  Transform bait intervals into targets more suitable for CNVkit.

- access

  List the locations of accessible sequence regions in a FASTA file.

- antitarget

  Derive off-target ("antitarget") bins from target regions.

- autobin

  Quickly calculate reasonable bin sizes from BAM read counts.

- coverage

  Calculate coverage in the given regions from BAM read depths.

- reference

  Compile a coverage reference from the given files (normal samples).

- fix

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

- segment

  Infer copy number segments from the given coverage table.

- call

  Call copy number variants from segmented log2 ratios.

- diagram

  Draw copy number (log2 coverages, segments) on chromosomes as a diagram. If both the raw probes and segments are given, show them side-by-side on each chromosome (segments on the left side, probes on the right side).

- scatter

  Plot probe log2 coverages and segmentation calls together.

- heatmap

  Plot copy number for multiple samples as a heatmap.

- breaks

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

- genemetrics

  Identify targeted genes with copy number gain or loss.

- sex

  Guess samples' sex from the relative coverage of chromosomes X and Y.

- metrics

  Compute coverage deviations and other metrics for self-evaluation.

- segmetrics

  Compute segment-level metrics from bin-level log2 ratios.

- bintest

  Test for single-bin copy number alterations.

- import-picard

  Convert Picard CalculateHsMetrics tabular output to CNVkit .cnn files. The input file is generated by the PER\_TARGET\_COVERAGE option in the CalculateHsMetrics script in Picard tools. If 'antitarget' is in the input filename, the generated output filename will have the suffix '.antitargetcoverage.cnn', otherwise '.targetcoverage.cnn'.

- import-seg

  Convert a SEG file to CNVkit .cns files.

- import-theta

  Convert THetA output to a BED-like, CNVkit-like tabular format. Equivalently, use the THetA results file to convert CNVkit .cns segments to integer copy number calls.

- import-rna

  Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.

- export

  Convert CNVkit output files to another format.

- version

  Display this program's version.

### options:

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

  show this help message and exit

See the online manual for details: https://cnvkit.readthedocs.io