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

# cnvkit-call(1)

Call copy number variants from segmented log2 ratios.

## NAME

cnvkit\_call - Call copy number variants from segmented log2 ratios.

## DESCRIPTION

usage: cnvkit.py call \[-h\] \[--center \[{mean,median,mode,biweight}\]\]

- \[--center-at CENTER\_AT\] \[--filter {ampdel,cn,ci,sem}\]

  \[-m {threshold,clonal,none}\] \[-t THRESHOLDS\] \[--ploidy PLOIDY\] \[--purity PURITY\] \[--drop-low-coverage\] \[-x {m,y,male,Male,f,x,female,Female}\] \[-y\] \[-o FILENAME\] \[-v FILENAME\] \[-i SAMPLE\_ID\] \[-n NORMAL\_ID\] \[--min-variant-depth MIN\_VARIANT\_DEPTH\] \[-z \[ALT\_FREQ\]\] filename

### positional arguments:

- filename

  Copy ratios (.cnr or .cns).

### options:

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

  show this help message and exit

- **--center** \[{mean,median,mode,biweight}\]

  Re-center the log2 ratio values using this estimator of the center or average value. ('median' if no argument given.)

- **--center-at** CENTER\_AT

  Subtract a constant number from all log2 ratios. For "manual" re-centering, in case the **--center** option gives unsatisfactory results.)

- **--filter** {ampdel,cn,ci,sem}

  Merge segments flagged by the specified filter(s) with the adjacent segment(s).

- **-m** {threshold,clonal,none}, **--method** {threshold,clonal,none}

  Calling method. \[Default: threshold\]

- **-t** THRESHOLDS, **--thresholds** THRESHOLDS

  Hard thresholds for calling each integer copy number, separated by commas. Use the '=' sign on the command line, e.g.: **-t**=*-1*,0,1 \[Default: **-1**.1,-0.25,0.2,0.7\]

- **--ploidy** PLOIDY

  Ploidy of the sample cells. \[Default: 2\]

- **--purity** PURITY

  Estimated tumor cell fraction, a.k.a. purity or cellularity.

- **--drop-low-coverage**

  Drop very-low-coverage bins before segmentation to avoid false-positive deletions in poor-quality tumor samples.

- **-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 sample's chromosomal sex as male or female. (Otherwise guessed from X and Y coverage).

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

  Was a male reference used? If so, expect half ploidy on chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit, if a male reference was used, the "neutral" copy number (ploidy) of chrX is 1; chrY is haploid for either reference sex.

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

  Output table file name (CNR-like table of segments, .cns).

### To additionally process SNP b-allele frequencies for allelic copy number:

- **-v** FILENAME, **--vcf** FILENAME

  VCF file name containing variants for calculation of b-allele frequencies.

- **-i** SAMPLE\_ID, **--sample-id** SAMPLE\_ID

  Name of the sample in the VCF (**-v**/--vcf) to use for b-allele frequency extraction.

- **-n** NORMAL\_ID, **--normal-id** NORMAL\_ID

  Corresponding normal sample ID in the input VCF (**-v**/--vcf). This sample is used to select only germline SNVs to calculate b-allele frequencies.

- **--min-variant-depth** MIN\_VARIANT\_DEPTH

  Minimum read depth for a SNV to be used in the b-allele frequency calculation. \[Default: 20\]

- **-z** \[ALT\_FREQ\], **--zygosity-freq** \[ALT\_FREQ\]

  Ignore VCF's genotypes (GT field) and instead infer zygosity from allele frequencies. \[Default if used without a number: 0.25\]