NAME

       cnvkit_scatter - Plot probe log2 coverages and segmentation calls together.

DESCRIPTION

       usage: cnvkit.py 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]  [--fig-size  WIDTH  HEIGHT]  [-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.

   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]