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| CNVKIT_SCATTER(1) |
User Commands |
CNVKIT_SCATTER(1) |
NAME¶
cnvkit_scatter - Plot probe log2 coverages and segmentation calls together.
DESCRIPTION¶
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]
positional arguments:¶
- filename
- Processed bin-level copy ratios (*.cnr), the output of the 'fix'
sub-command.
optional arguments:¶
- -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.
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]
