Generate Highlighted HTML for BAM
Project description
Generate Highlighted HTML of Bam
highlight the specific sites of html which output by
samtools tview
Dependencies
- Linux/Unix
- Samtools
- Python2/Python3
Examples
bam2html <input.bam> chrom:pos # single position
bam2html <input.bam> chrom:pos1,pos2... # multiple positions
bam2html <input.bam> chrom:start-end # a region of positions
bam2html <input.bam> chrom:pos -r /path/to/reference.fa # with reference
Meaning of Base's Colors
| Color | Mapping Quality | Selector |
|---|---|---|
| Blue | 0-9 | .tviewcu1 |
| Green | 10-19 | .tviewc2 |
| Yellow | 20-29 | .tviewc3 |
| Black | >=30 | .tviewc4 |
Underline: Secondary or orphan
Download files
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Source Distribution
bam2html-1.0.0.tar.gz
(5.6 kB
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