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

# cnvkit-reference(1)

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

## NAME

cnvkit\_reference - Compile a coverage reference from the given files (normal samples).

## DESCRIPTION

usage: cnvkit.py reference \[-h\] \[-f FASTA\] \[-o FILENAME\] \[-c\]

- \[--min-cluster-size NUM\]

  \[-x {m,y,male,Male,f,x,female,Female}\] \[-y\] \[-t TARGETS\] \[-a ANTITARGETS\] \[--no-gc\] \[--no-edge\] \[--no-rmask\] \[references ...\]

### positional arguments:

- references

  Normal-sample target or antitarget .cnn files, or the directory that contains them.

### options:

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

  show this help message and exit

- **-f** FASTA, **--fasta** FASTA

  Reference genome, FASTA format (e.g. UCSC hg19.fa)

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

  Output file name.

- **-c**, **--cluster**

  Calculate and store summary stats for clustered subsets of the normal samples with similar coverage profiles.

- **--min-cluster-size** NUM

  Minimum cluster size to keep in reference profiles. \[Default: 4\]

- **-x** {m,y,male,Male,f,x,female,Female}, **--sample-sex** {m,y,male,Male,f,x,female,Female}, **-g** {m,y,male,Male,f,x,female,Female}, **--gender** {m,y,male,Male,f,x,female,Female}

  Specify the chromosomal sex of all given samples as male or female. (Default: guess each sample from coverage of X and Y chromosomes).

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

  Create a male reference: shift female samples' chrX log-coverage by **-1**, so the reference chrX average is **-1**. Otherwise, shift male samples' chrX by +1, so the reference chrX average is 0.

### To construct a generic, flat" copy number reference with neutral expected coverage:"

- **-t** TARGETS, **--targets** TARGETS

  Target intervals (.bed or .list)

- **-a** ANTITARGETS, **--antitargets** ANTITARGETS

  Antitarget intervals (.bed or .list)

### To disable specific automatic bias corrections:

- **--no-gc**

  Skip GC correction.

- **--no-edge**

  Skip edge-effect correction.

- **--no-rmask**

  Skip RepeatMasker correction.