bam2html 1.0.5
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Description:
bam2html 1.0.5
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
Documents
https://bam2html.readthedocs.io
License:
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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