3. Optional arguments¶

`-h, --help`	show this help message and exit
`-v, --version`	show program’s version number and exit
`-silence`	don’t print any log.
`-debug`	turn on debugging mode
`-process`	number of process for multi-processing (default=1)

3.1. Input files¶

`-bam`	bam file(s) to use
`-bamlist`	file listing bam files to use
`-title`	label(s) to be used as title for bam file(s)
`-no_title`	(default: false) do not draw title
`-title_fontsize`
	(default=18) font size of title
`-pos`	genomic position(s) to plot
`-vcf`	file listing genomic positions to plot in VCF format
`-bed`	file listing genomic positions to plot in BED format
`-ref`	reference sequence as fasta file
`-ref_index_rebuild`
	(default=false) rebuild fasta index file (.fai)
`-refversion`	[hg38, hg19] (default=hg38) reference version
`-conf`	`configuration file`_

3.2. Output file¶

`-out`	output file name or title of output file
`-imagetype`	[png, jpg] (default=png) output file type
`-save_image_only`
	(default=false) save image only
`-image_dir_name`
	image directory name
`-zipout`	(default=false) make a single zip file
`-separated_bam`	(default=false) draw a plot for each bam

3.3. Plot layout¶

`-draw`	(default=coordinates bamplot base gene) track composition
`-bamplot`	(default=coverage base read) track composition in bamplot
`-width`	(default=1000) image width (unit:px)
`-height`	image height (unit:px)
`-bgcolor`	(default=FFFFFF) background color
`-plot_margin_top`
	(default=20) top margin size of plot
`-plot_margin_bottom`
	(default=20) bottom margin size of plot
`-plot_margin_left`
	(default=0) left margin size of plot
`-plot_margin_right`
	(default=0) right margin size of plot
`-border`	(default=false) draw border in plot
`-separator_height`
	(default=30) separator’s height

3.4. Read alignment track¶

`-read_thickness`
	(default=5) read thickness (unit:px)
`-read_gap_height`
	(default=2) read gap height (unit:px)
`-read_gap_width`
	(default=2) read gap width (unit:px)
`-read_bgcolor`	(default=FFFFFF) read background color
`-read_color`	(default=C8C8C8) read color
`-margin`	(default=50) genomic margin size
`-center_line`	(default=false) draw center line
`-no_target_line`
	(default=false) do not draw target line
`-read_group`	[‘’, strand] (default=’’) read color
`-read_pos_color`
	(default=FFAC9C) positive strand read color
`-read_neg_color`
	(default=A19CFF) negative strand read color
`-read_color_by`	[‘’, strand, intercom] (default=’’) read color by
`-read_color_interchrom_chr1`
	(default=64689b) paired read color located in chromosome 1
`-read_color_interchrom_chr2`
	(default=D6503A) paired read color located in chromosome 2
`-read_color_interchrom_chr3`
	(default=87AA62) paired read color located in chromosome 3
`-read_color_interchrom_chr4`
	(default=F2EB89) paired read color located in chromosome 4
`-read_color_interchrom_chr5`
	(default=597E98) paired read color located in chromosome 5
`-read_color_interchrom_chr6`
	(default=C5763E) paired read color located in chromosome 6
`-read_color_interchrom_chr7`
	(default=70BFE7) paired read color located in chromosome 7
`-read_color_interchrom_chr8`
	(default=91307F) paired read color located in chromosome 8
`-read_color_interchrom_chr9`
	(default=80DE6E) paired read color located in chromosome 9
`-read_color_interchrom_chr10`
	(default=DCA5B5) paired read color located in chromosome 10
`-read_color_interchrom_chr11`
	(default=A35A24) paired read color located in chromosome 11
`-read_color_interchrom_chr12`
	(default=978DA0) paired read color located in chromosome 12
`-read_color_interchrom_chr13`
	(default=D16525) paired read color located in chromosome 13
`-read_color_interchrom_chr14`
	(default=DCA167) paired read color located in chromosome 14
`-read_color_interchrom_chr15`
	(default=8C79B9) paired read color located in chromosome 15
`-read_color_interchrom_chr16`
	(default=E9BD71) paired read color located in chromosome 16
`-read_color_interchrom_chr17`
	(default=4B2669) paired read color located in chromosome 17
`-read_color_interchrom_chr18`
	(default=D7E4BF) paired read color located in chromosome 18
`-read_color_interchrom_chr19`
	(default=733B91) paired read color located in chromosome 19
`-read_color_interchrom_chr20`
	(default=BC2D7A) paired read color located in chromosome 20
`-read_color_interchrom_chr21`
	(default=EBD176) paired read color located in chromosome 21
`-read_color_interchrom_chr22`
	(default=6E786F) paired read color located in chromosome 22
`-read_color_interchrom_chrX`
	(default=D5AA00) paired read color located in chromosome X
`-read_color_interchrom_chrY`
	(default=A9D400) paired read color located in chromosome Y
`-show_soft_clipped`
	(default=False) show soft clipped part

3.5. Base track¶

`-base_fontsize`	(default=9) font size of base
`-base_height`	(default=30) base track height
`-base_margin_top`
	(default=0) top margin size of base track
`-base_margin_bottom`
	(default=0) bottom margin size of base track

3.6. Coverage track¶

`-coverage_height`
	(default=40) coverage track height
`-coverage_fontsize`
	(default=9) coverage font size
`-coverage_vaf`	(default=0.2) coverage variant allele fraction threshold
`-coverage_color`
	(default=C8C8C8) coverage color
`-coverage_bgcolor`
	(default=FFFFFF) coverage track background color

3.7. Heatmap track¶

`-heatmap_height`
	(default=5) coverage heatmap height
`-heatmap_bgcolor`
	(default=FFFFFF) coverage heatmap track background color

3.8. Gene track¶

`-gene_height`	(default=50) gene track height
`-gene_fontsize`	(default=10) font size of gene track
`-gene_pos_color`
	(default=FFAC9C) positive strand color
`-gene_neg_color`
	(default=A19CFF) negative strand color

3.9. Coordinates track¶

`-coordinates_height`
	(default=20) coordinates height
`-coordinates_fontsize`
	(default=12) coordinates font size
`-coordinates_axisloc`
	[top, bottom, middle] (default=bottom) coordinates axis location
`-coordinates_bgcolor`
	(default=FFFFFF) coordinates background color
`-coordinates_labelcolor`
	(default=000000) coordinates label color