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

# cnvkit-scatter(1)

Plot probe log2 coverages and segmentation calls together.

## NAME

cnvkit\_scatter - Plot probe log2 coverages and segmentation calls together.

## DESCRIPTION

usage: cnvkit.py scatter \[-h\] \[-s FILENAME\] \[-c RANGE\] \[-g GENE\]

- \[-l RANGE\_LIST\] \[-w WIDTH\] \[-o FILENAME\]

  \[-a CHARACTER\] \[--by-bin\] \[--segment-color SEGMENT\_COLOR\] \[--title TITLE\] \[-t\] \[--y-max Y\_MAX\] \[--y-min Y\_MIN\] \[--fig-size WIDTH HEIGHT\] \[-v FILENAME\] \[-i SAMPLE\_ID\] \[-n NORMAL\_ID\] \[-m MIN\_VARIANT\_DEPTH\] \[-z \[ALT\_FREQ\]\] \[filename\]

### positional arguments:

- filename

  Processed bin-level copy ratios (\*.cnr), the output of the 'fix' sub-command.

### options:

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

  show this help message and exit

- **-s** FILENAME, **--segment** FILENAME

  Segmentation calls (.cns), the output of the 'segment' command.

- **-c** RANGE, **--chromosome** RANGE

  Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000', to display. If a range is given, all targeted genes in this range will be shown, unless **-g**/--gene is also given.

- **-g** GENE, **--gene** GENE

  Name of gene or genes (comma-separated) to display.

- **-l** RANGE\_LIST, **--range-list** RANGE\_LIST

  File listing the chromosomal ranges to display, as BED, interval list or 'chr:start-end' text. Creates focal plots similar to **-c**/--chromosome for each listed region, combined into a multi-page PDF. The output filename must also be specified (**-o**/--output).

- **-w** WIDTH, **--width** WIDTH

  Width of margin to show around the selected gene(s) (**-g**/--gene) or small chromosomal region (**-c**/--chromosome). \[Default: 1000000\]

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

  Output PDF file name.

### Plot aesthetics:

- **-a** CHARACTER, **--antitarget-marker** CHARACTER

  Plot antitargets using this symbol when plotting in a selected chromosomal region (**-g**/--gene or **-c**/--chromosome). \[Default: same as targets\]

- **--by-bin**

  Plot data x-coordinates by bin indices instead of genomic coordinates. All bins will be shown with equal width, no blank regions will be shown, and x-axis values indicate bin number (within chromosome) instead of genomic position.

- **--segment-color** SEGMENT\_COLOR

  Plot segment lines in this color. Value can be any string accepted by matplotlib, e.g. 'red' or '#CC0000'.

- **--title** TITLE

  Plot title. \[Default: sample ID, from filename or **-i\]**

- **-t**, **--trend**

  Draw a smoothed local trendline on the scatter plot.

- **--y-max** Y\_MAX

  y-axis upper limit.

- **--y-min** Y\_MIN

  y-axis lower limit.

- **--fig-size** WIDTH HEIGHT

  Width and height of the plot in inches. \[Default: Predefined in Matplotlib 'rcParams' variable (most of the time: '6.4 4.8')\]

### To plot SNP b-allele frequencies:

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

  VCF file name containing variants to plot for SNV b-allele frequencies.

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

  Name of the sample in the 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. This sample is used to select only germline SNVs to plot.

- **-m** MIN\_VARIANT\_DEPTH, **--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. \[Default if used without a number: 0.25\]