DOKK / manpages / debian 10 / cnvkit / cnvkit-scatter.1.en

cnvkit_scatter - Plot probe log2 coverages and segmentation calls together.

usage: cnvkit scatter [-h] [-s FILENAME] [-c RANGE] [-g GENE] [-l RANGE_LIST]

[-w WIDTH] [-o FILENAME] [-a CHARACTER] [--by-bin]
[--segment-color SEGMENT_COLOR] [--title TITLE] [-t] [--y-max Y_MAX] [--y-min Y_MIN] [-v FILENAME] [-i SAMPLE_ID] [-n NORMAL_ID] [-m MIN_VARIANT_DEPTH] [-z [ALT_FREQ]] [filename]

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

show this help message and exit
Segmentation calls (.cns), the output of the 'segment' command.
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.
Name of gene or genes (comma-separated) to display.
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).
Width of margin to show around the selected gene(s) (-g/--gene) or small chromosomal region (-c/--chromosome). [Default: 1000000]
Output PDF file name.

Plot antitargets using this symbol when plotting in a selected chromosomal region (-g/--gene or -c/--chromosome). [Default: same as targets]
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.
Plot segment lines in this color. Value can be any string accepted by matplotlib, e.g. 'red' or '#CC0000'.
Plot title. [Default: sample ID, from filename or -i]
Draw a smoothed local trendline on the scatter plot.
y-axis upper limit.
y-axis lower limit.

VCF file name containing variants to plot for SNV b-allele frequencies.
Name of the sample in the VCF to use for b-allele frequency extraction and as the default plot title.
Corresponding normal sample ID in the input VCF. This sample is used to select only germline SNVs to plot.
Minimum read depth for a SNV to be used in the b-allele frequency calculation. [Default: 20]
Ignore VCF's genotypes (GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25]
March 2019 cnvkit_scatter 0.9.5