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View Bam in Highlighted HTML

Project description

DOI GitHub (Pre-)Release Date

Generate Highlighted HTML of Bam

highlight the specific sites of bam with samtools tview


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


pip install bam2html


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

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


Project details

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Source Distribution

bam2html-1.0.5.tar.gz (9.1 kB view hashes)

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