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]