cnvkit-scatter1

positional arguments:

filename

Processed bin-level copy ratios (*.cnr), the output of the 'fix' sub-command.

options:

-h, --help

show this help message and exit

-s FILENAME, --segment FILENAME

Segmentation calls (.cns), the output of the 'segment' command.

-c RANGE, --chromosome RANGE

Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000', to display. If a range is given, all targeted genes in this range will be shown, unless -g/--gene is also given.

-g GENE, --gene GENE

Name of gene or genes (comma-separated) to display.

-l RANGE_LIST, --range-list RANGE_LIST

File listing the chromosomal ranges to display, as BED, interval list or 'chr:start-end' text. Creates focal plots similar to -c/--chromosome for each listed region, combined into a multi-page PDF. The output filename must also be specified (-o/--output).

-w WIDTH, --width WIDTH

Width of margin to show around the selected gene(s) (-g/--gene) or small chromosomal region (-c/--chromosome). [Default: 1000000]

-o FILENAME, --output FILENAME

Output PDF file name.

Plot aesthetics:

-a CHARACTER, --antitarget-marker CHARACTER

Plot antitargets using this symbol when plotting in a selected chromosomal region (-g/--gene or -c/--chromosome). [Default: same as targets]

--by-bin

Plot data x-coordinates by bin indices instead of genomic coordinates. All bins will be shown with equal width, no blank regions will be shown, and x-axis values indicate bin number (within chromosome) instead of genomic position.

--segment-color SEGMENT_COLOR

Plot segment lines in this color. Value can be any string accepted by matplotlib, e.g. 'red' or '#CC0000'.

--title TITLE

Plot title. [Default: sample ID, from filename or -i]

-t, --trend

Draw a smoothed local trendline on the scatter plot.

--y-max Y_MAX

y-axis upper limit.

--y-min Y_MIN

y-axis lower limit.

--fig-size WIDTH HEIGHT

Width and height of the plot in inches. [Default: Predefined in Matplotlib 'rcParams' variable (most of the time: '6.4 4.8')]

To plot SNP b-allele frequencies:

-v FILENAME, --vcf FILENAME

VCF file name containing variants to plot for SNV b-allele frequencies.

-i SAMPLE_ID, --sample-id SAMPLE_ID

Name of the sample in the VCF to use for b-allele frequency extraction and as the default plot title.

-n NORMAL_ID, --normal-id NORMAL_ID

Corresponding normal sample ID in the input VCF. This sample is used to select only germline SNVs to plot.

-m MIN_VARIANT_DEPTH, --min-variant-depth MIN_VARIANT_DEPTH

Minimum read depth for a SNV to be used in the b-allele frequency calculation. [Default: 20]

-z [ALT_FREQ], --zygosity-freq [ALT_FREQ]

Ignore VCF's genotypes (GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25]