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CNVKIT_DIAGRAM(1) User Commands CNVKIT_DIAGRAM(1)

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:

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

options:

show this help message and exit
Segmentation calls (.cns), the output of the 'segment' command.
Chromosome to display, e.g. 'chr1' (no chromosomal range allowed)
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 aesthetics:

Plot title. [Default: sample ID, from filename or -i]
Disable gene_name labels on plot (useful when a lot of CNV were called).
July 2023 cnvkit.py diagram 0.9.10