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

# cnvkit-segment(1)

Infer copy number segments from the given coverage table.

## NAME

cnvkit\_segment - Infer copy number segments from the given coverage table.

## DESCRIPTION

usage: cnvkit.py segment \[-h\] \[-o FILENAME\] \[-d DATAFRAME\]

- \[-m {cbs,flasso,haar,none,hmm,hmm-tumor,hmm-germline}\]

  \[-t THRESHOLD\] \[--drop-low-coverage\] \[--drop-outliers FACTOR\] \[--rscript-path PATH\] \[-p \[PROCESSES\]\] \[--smooth-cbs\] \[-v FILENAME\] \[-i SAMPLE\_ID\] \[-n NORMAL\_ID\] \[--min-variant-depth MIN\_VARIANT\_DEPTH\] \[-z \[ALT\_FREQ\]\] filename

### positional arguments:

- filename

  Bin-level log2 ratios (.cnr file), as produced by 'fix'.

### options:

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

  show this help message and exit

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

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

- **-d** DATAFRAME, **--dataframe** DATAFRAME

  File name to save the raw R dataframe emitted by CBS or Fused Lasso. (Useful for debugging.)

- **-m** {cbs,flasso,haar,none,hmm,hmm-tumor,hmm-germline}, **--method** {cbs,flasso,haar,none,hmm,hmm-tumor,hmm-germline}

  Segmentation method (see docs), or 'none' for chromosome arm-level averages as segments. \[Default: cbs\]

- **-t** THRESHOLD, **--threshold** THRESHOLD

  Significance threshold (p-value or FDR, depending on method) to accept breakpoints during segmentation. For HMM methods, this is the smoothing window size.

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

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

- **--drop-outliers** FACTOR

  Drop outlier bins more than this many multiples of the 95th quantile away from the average within a rolling window. Set to 0 for no outlier filtering. \[Default: 10\]

- **--rscript-path** PATH

  Path to the Rscript executable to use for running R code. Use this option to specify a non-default R installation. \[Default: Rscript\]

- **-p** \[PROCESSES\], **--processes** \[PROCESSES\]

  Number of subprocesses to segment in parallel. Give 0 or a negative value to use the maximum number of available CPUs. \[Default: use 1 process\]

- **--smooth-cbs**

  Perform an additional smoothing before CBS segmentation, which in some cases may increase the sensitivity. Used only for CBS method.

### To additionally segment SNP b-allele frequencies:

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

  VCF file name containing variants for segmentation by allele frequencies.

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

  Specify the name of the sample in the VCF (**-v**/--vcf) to use for b-allele frequency extraction and as the default plot title.

- **-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 plot b-allele frequencies.

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

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

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

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