Advanced Options

This page documents the use of the advanced options in samplot plot. This will include nearly all possible parameters to samplot plot that are not explained in the Basic Options page.

  -z Z, --z Z           Number of stdevs from the mean (default 4)
                        Space-delimited list of BAM/CRAM file names
  -o OUTPUT_FILE, --output_file OUTPUT_FILE
                        Output file name/type. Defaults to
                        {type}_{chrom}_{start}_{end}.png
  --output_dir OUTPUT_DIR
                        Output directory name. Defaults to working dir.
                        Ignored if --output_file is set
  -w WINDOW, --window WINDOW
                        Window size (count of bases to include in view),
                        default(0.5 * len)
  -d MAX_DEPTH, --max_depth MAX_DEPTH
                        Max number of normal pairs to plot
  -T TRANSCRIPT_FILE, --transcript_file TRANSCRIPT_FILE
                        GFF3 of transcripts
  --transcript_filename TRANSCRIPT_FILENAME
                        Name for transcript track
  --max_coverage_points MAX_COVERAGE_POINTS
                        number of points to plot in coverage axis (downsampled
                        from region size for speed)
  -A ANNOTATION_FILES [ANNOTATION_FILES ...], --annotation_files ANNOTATION_FILES [ANNOTATION_FILES ...]
                        Space-delimited list of bed.gz tabixed files of
                        annotations (such as repeats, mappability, etc.)
  --annotation_filenames ANNOTATION_FILENAMES [ANNOTATION_FILENAMES ...]
                        Space-delimited list of names for the tracks in
                        --annotation_files
  --coverage_tracktype {stack,superimpose,none}
                        type of track to use for low MAPQ coverage plot.
  -a, --print_args      Print commandline arguments to a json file, useful
                        with PlotCritic
  -H PLOT_HEIGHT, --plot_height PLOT_HEIGHT
                        Plot height
  -W PLOT_WIDTH, --plot_width PLOT_WIDTH
                        Plot width
  -q INCLUDE_MQUAL, --include_mqual INCLUDE_MQUAL
                        Min mapping quality of reads to be included in plot
                        (default 1)
  --separate_mqual SEPARATE_MQUAL
                        coverage from reads with MAPQ <= separate_mqual
                        plotted in lighter grey. To disable, pass in negative
                        value
  -j, --json_only       Create only the json file, not the image plot
  --start_ci START_CI   confidence intervals of SV first breakpoint (distance
                        from the breakpoint). Must be a comma-separated pair
                        of ints (i.e. 20,40)
  --end_ci END_CI       confidence intervals of SV end breakpoint (distance
                        from the breakpoint). Must be a comma-separated pair
                        of ints (i.e. 20,40)
  --long_read LONG_READ
                        Min length of a read to be treated as a long-read
                        (default 1000)
  --ignore_hp           Choose to ignore HP tag in alignment files
  --min_event_size MIN_EVENT_SIZE
                        Min size of an event in long-read CIGAR to include
                        (default 20)
  --xaxis_label_fontsize XAXIS_LABEL_FONTSIZE
                        Font size for X-axis labels (default 6)
  --yaxis_label_fontsize YAXIS_LABEL_FONTSIZE
                        Font size for Y-axis labels (default 6)
  --legend_fontsize LEGEND_FONTSIZE
                        Font size for legend labels (default 6)
  --annotation_fontsize ANNOTATION_FONTSIZE
                        Font size for annotation labels (default 6)
  --common_insert_size  Set common insert size for all plots
  --hide_annotation_labels
                        Hide the label (fourth column text) from annotation
                        files, useful for regions with many annotations
  --coverage_only       Hide all reads and show only coverage
  --max_coverage MAX_COVERAGE
                        apply a maximum coverage cutoff. Unlimited by default
  --same_yaxis_scales   Set the scales of the Y axes to the max of all
  --marker_size MARKER_SIZE
                        Size of marks on pairs and splits (default 3)
  --dpi DPI             Dots per inches (pixel count, default 300)
  --annotation_scalar ANNOTATION_SCALAR
                        scaling factor for the optional annotation/transcript
                        tracks
  --zoom ZOOM           Only show +- zoom amount around breakpoints, much
                        faster for large regions. Ignored if region smaller
                        than --zoom (default 500000)
  --debug DEBUG         Print debug statements