highlight the specific sites of bam with
samtools tview
- Linux/Unix
- Python2/Python3
- samtools
- tar/gzip/zip [optional for compressing]
pip install bam2htmlbam2html -b <input.bam> chrom:pos # single position
bam2html -b <input.bam> chrom:pos1,pos2... # multiple positions
bam2html -b <input.bam> chrom:start-end # a region of positions
bam2html -b <input.bam> chrom:pos -r /path/to/reference.fa # with reference
bam2html -b <input.bam> chrom:pos -c 300 # set the width of window
bam2html -b <input.bam> chrom:pos -color pink -bg green # set colors
bam2html -bl bam_list pos_list # batch mode
bam2html -bl bam_list pos_list -s # generate summary.html
bam2html -bl bam_list pos_list -s -x zip # compress the result with zip
bam2html -bl bam_list pos_list -s -x tar.gz # compress the result with tar/gzip- single position: demo.1_985460.html
- multiple positions: demo.1_985460,985463,985469.html
- region positions: demo.1_985461-985465.html
- summary result: summary.html
| Color | Mapping Quality | Selector |
|---|---|---|
| Blue | 0-9 | .tviewcu1 |
| Green | 10-19 | .tviewc2 |
| Yellow | 20-29 | .tviewc3 |
| Black | >=30 | .tviewc4 |
Underline: Secondary or orphan