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 |