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

# cnvkit-diagram(1)

Draw copy number (log2 coverages, segments) on chromosomes as a diagram. If both the raw probes and segments are given, show them side-by-side on each chromosome (segments on the left side, probes on the right side).

## NAME

cnvkit\_diagram - Draw copy number (log2 coverages, segments) on chromosomes as a diagram.

    If both the raw probes and segments are given, show them side-by-side on\
     each chromosome (segments on the left side, probes on the right side).

## DESCRIPTION

usage: cnvkit.py diagram \[-h\] \[-s SEGMENT\] \[-c CHROMOSOME\] \[-t THRESHOLD\]

- \[-m MIN\_PROBES\] \[-y\]

  \[-x {m,y,male,Male,f,x,female,Female}\] \[--no-shift-xy\] \[-o FILENAME\] \[--title TITLE\] \[--no-gene-labels\] \[filename\]

### positional arguments:

- filename

  Processed coverage data file (\*.cnr), the output of the 'fix' sub-command.

### options:

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

  show this help message and exit

- **-s** SEGMENT, **--segment** SEGMENT

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

- **-c** CHROMOSOME, **--chromosome** CHROMOSOME

  Chromosome to display, e.g. 'chr1' (no chromosomal range allowed)

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

  Copy number change threshold to label genes. \[Default: 0.5\]

- **-m** MIN\_PROBES, **--min-probes** MIN\_PROBES

  Minimum number of covered probes to label a gene. \[Default: 3\]

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

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

- **-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).

- **--no-shift-xy**

  Don't adjust the X and Y chromosomes according to sample sex.

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

  Output PDF file name.

### Plot aesthetics:

- **--title** TITLE

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

- **--no-gene-labels**

  Disable gene\_name labels on plot (useful when a lot of CNV were called).