bam2html

Generate Highlighted HTML of Bam

highlight the specific sites of bam with samtools tview

Dependencies

• Linux/Unix
• Python2/Python3
• samtools
• tar/gzip/zip [optional for compressing]

Installation

pip install bam2html

Usage

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 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

Example Results

• 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

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

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Documents

https://bam2html.readthedocs.io