NAME¶
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).
DESCRIPTION¶
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]
positional arguments:¶
- filename
- Processed coverage data file (*.cnr), the output of the 'fix'
sub-command.
optional arguments:¶
- -h, --help
- show this help message and exit
- -s SEGMENT, --segment SEGMENT
- Segmentation calls (.cns), the output of the 'segment' command.
- -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]
