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

# cnvkit-import-seg(1)

Convert a SEG file to CNVkit .cns files.

## NAME

cnvkit\_import-seg - Convert a SEG file to CNVkit .cns files.

## DESCRIPTION

usage: cnvkit.py import-seg \[-h\] \[-c CHROMOSOMES\] \[-p PREFIX\] \[--from-log10\]

- \[-d DIRECTORY\]

  segfile

### positional arguments:

- segfile

  Input file in SEG format. May contain multiple samples.

### options:

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

  show this help message and exit

- **-c** CHROMOSOMES, **--chromosomes** CHROMOSOMES

  Mapping of chromosome indexes to names. Syntax: "from1:to1,from2:to2". Or use "human" for the preset: "23:X,24:Y,25:M".

- **-p** PREFIX, **--prefix** PREFIX

  Prefix to add to chromosome names (e.g 'chr' to rename '8' in the SEG file to 'chr8' in the output).

- **--from-log10**

  Convert base-10 logarithm values in the input to base-2 logs.

- **-d** DIRECTORY, **--output-dir** DIRECTORY

  Output directory name.