Man page - cnvkit-diagram(1)
Packages contains this manual
- cnvkit-import-theta(1)
- cnvkit-coverage(1)
- cnvkit-metrics(1)
- cnvkit-import-seg(1)
- cnvkit-export(1)
- cnvkit-breaks(1)
- cnvkit-fix(1)
- cnvkit-segmetrics(1)
- cnvkit-batch(1)
- cnvkit-import-rna(1)
- cnvkit-bintest(1)
- cnvkit-diagram(1)
- cnvkit-call(1)
- cnvkit-autobin(1)
- cnvkit-access(1)
- cnvkit-antitarget(1)
- cnvkit-sex(1)
- cnvkit-segment(1)
- cnvkit-genemetrics(1)
- cnvkit-heatmap(1)
- cnvkit-target(1)
- cnvkit-import-picard(1)
- cnvkit-reference(1)
- cnvkit-scatter(1)
apt-get install cnvkit
Manual
CNVKIT_DIAGRAM
NAMEDESCRIPTION
positional arguments:
options:
Plot aesthetics:
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).