cnvkit-diagram1

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).