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

# cnvkit-export(1)

Convert CNVkit output files to another format.

## NAME

cnvkit\_export - Convert CNVkit output files to another format.

## DESCRIPTION

usage: cnvkit.py export \[-h\]

- {bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv,gistic}

  ...

### positional arguments:

- {bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv,gistic}

  Export formats (use with **-h** for more info).

- bed

  Convert segments to BED format. Input is a segmentation file (.cns) where, preferably, log2 ratios have already been adjusted to integer absolute values using the 'call' command.

- seg

  Convert segments to SEG format. Compatible with IGV and GenePattern.

- vcf

  Convert segments to VCF format. Input is a segmentation file (.cns) where, preferably, log2 ratios have already been adjusted to integer absolute values using the 'call' command.

- theta

  Convert segments to THetA2 input file format (\*.input).

- nexus-basic

  Convert bin-level log2 ratios to Nexus Copy Number "basic" format.

- nexus-ogt

  Convert log2 ratios and b-allele freqs to Nexus "Custom-OGT" format.

- cdt

  Convert log2 ratios to CDT format. Compatible with Java TreeView.

- jtv

  Convert log2 ratios to Java TreeView's native format.

-

  gistic

### options:

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

  show this help message and exit