DOKK / manpages / debian 10 / cnvkit / cnvkit-diagram.1.en

cnvkit_diagram - Draw copy number (log2 coverages, CBS calls) 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).

usage: cnvkit diagram [-h] [-s SEGMENT] [-t THRESHOLD] [-m MIN_PROBES] [-y]

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

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

show this help message and exit
Segmentation calls (.cns), the output of the 'segment' command.
Copy number change threshold to label genes. [Default: 0.5]
Minimum number of covered probes to label a gene. [Default: 3]
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).
Specify the sample's chromosomal sex as male or female. (Otherwise guessed from X and Y coverage).
Don't adjust the X and Y chromosomes according to sample sex.
Output PDF file name.

Plot title. [Default: sample ID, from filename or -i]
March 2019 cnvkit_diagram 0.9.5