为BAM生成突出显示的HTML
bam2html的Python项目详细描述
生成Bam突出显示的HTML
highlight the specific sites of html which output by
samtools tview
依赖关系
- Linux/Unix系统
- Samtools公司
- Python2/Python3
- tar/gzip/zip[压缩可选]
使用
bam2html -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 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
示例结果
- 单一位置：demo.1_985460.html
- 多个位置：demo.1_985460,985463,985469.html
- 区域位置：demo.1_985461-985465.html
- 摘要结果：summary.html
底色的意义
| Color | Mapping Quality | Selector |
|---|---|---|
| Blue | 0-9 | .tviewcu1 |
| Green | 10-19 | .tviewc2 |
| Yellow | 20-29 | .tviewc3 |
| Black | >=30 | .tviewc4 |
Underline: Secondary or orphan
文件
https://bam2html.readthedocs.io
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