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

# cnvkit-sex(1)

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

## NAME

cnvkit\_sex - Guess samples' sex from the relative coverage of chromosomes X and Y.

## DESCRIPTION

usage: cnvkit.py sex \[-h\] \[-y\] \[-o FILENAME\] filenames \[filenames ...\]

### positional arguments:

- filenames

  Copy number or copy ratio files (\*.cnn, \*.cnr).

### options:

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

  show this help message and exit

- **-y**, **--male-reference**, **--haploid-x-reference**

  Assume inputs were normalized to a male reference (i.e. female samples will have +1 log-coverage of chrX; otherwise male samples would have **-1** chrX).

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

  Output table file name.