.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH CNVKIT_SCATTER "1" "January 2021" "cnvkit scatter 0.9.8" "User Commands"
.SH NAME
cnvkit_scatter \- Plot probe log2 coverages and segmentation calls together.
.SH DESCRIPTION
usage: cnvkit scatter [\-h] [\-s FILENAME] [\-c RANGE] [\-g GENE] [\-l RANGE_LIST]
.TP
[\-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]
.SS "positional arguments:"
.TP
filename
Processed bin\-level copy ratios (*.cnr), the output of
the 'fix' sub\-command.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-s\fR FILENAME, \fB\-\-segment\fR FILENAME
Segmentation calls (.cns), the output of the 'segment'
command.
.TP
\fB\-c\fR RANGE, \fB\-\-chromosome\fR 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 \fB\-g\fR/\-\-gene is also given.
.TP
\fB\-g\fR GENE, \fB\-\-gene\fR GENE
Name of gene or genes (comma\-separated) to display.
.TP
\fB\-l\fR RANGE_LIST, \fB\-\-range\-list\fR RANGE_LIST
File listing the chromosomal ranges to display, as
BED, interval list or 'chr:start\-end' text. Creates
focal plots similar to \fB\-c\fR/\-\-chromosome for each listed
region, combined into a multi\-page PDF. The output
filename must also be specified (\fB\-o\fR/\-\-output).
.TP
\fB\-w\fR WIDTH, \fB\-\-width\fR WIDTH
Width of margin to show around the selected gene(s)
(\fB\-g\fR/\-\-gene) or small chromosomal region
(\fB\-c\fR/\-\-chromosome). [Default: 1000000]
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output PDF file name.
.SS "Plot aesthetics:"
.TP
\fB\-a\fR CHARACTER, \fB\-\-antitarget\-marker\fR CHARACTER
Plot antitargets using this symbol when plotting in a
selected chromosomal region (\fB\-g\fR/\-\-gene or
\fB\-c\fR/\-\-chromosome). [Default: same as targets]
.TP
\fB\-\-by\-bin\fR
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.
.TP
\fB\-\-segment\-color\fR SEGMENT_COLOR
Plot segment lines in this color. Value can be any
string accepted by matplotlib, e.g. 'red' or
\&'#CC0000'.
.TP
\fB\-\-title\fR TITLE
Plot title. [Default: sample ID, from filename or \fB\-i]\fR
.TP
\fB\-t\fR, \fB\-\-trend\fR
Draw a smoothed local trendline on the scatter plot.
.TP
\fB\-\-y\-max\fR Y_MAX
y\-axis upper limit.
.TP
\fB\-\-y\-min\fR Y_MIN
y\-axis lower limit.
.SS "To plot SNP b-allele frequencies:"
.TP
\fB\-v\fR FILENAME, \fB\-\-vcf\fR FILENAME
VCF file name containing variants to plot for SNV
b\-allele frequencies.
.TP
\fB\-i\fR SAMPLE_ID, \fB\-\-sample\-id\fR SAMPLE_ID
Name of the sample in the VCF to use for b\-allele
frequency extraction and as the default plot title.
.TP
\fB\-n\fR NORMAL_ID, \fB\-\-normal\-id\fR NORMAL_ID
Corresponding normal sample ID in the input VCF. This
sample is used to select only germline SNVs to plot.
.TP
\fB\-m\fR MIN_VARIANT_DEPTH, \fB\-\-min\-variant\-depth\fR MIN_VARIANT_DEPTH
Minimum read depth for a SNV to be used in the
b\-allele frequency calculation. [Default: 20]
.TP
\fB\-z\fR [ALT_FREQ], \fB\-\-zygosity\-freq\fR [ALT_FREQ]
Ignore VCF's genotypes (GT field) and instead infer
zygosity from allele frequencies. [Default if used
without a number: 0.25]