Tutorials

highlight single position

bam2html -r reference.fa -b demo.bam 1:12345
bam2html -r reference.fa -b demo.bam 1:12345 2:45678

highlight multiple positions in one file

bam2html -r reference.fa -b demo.bam 1:12345,12347
bam2html -r reference.fa -b demo.bam 1:12345,12349 2:45678,45681

highlight a region

bam2html -r reference.fa -b demo.bam 1:12345-12350

highlight in batch mode

# multiple bams separated by comma
bam2html -r reference.fa -b demo.bam,demo2.bam 1:12345 2:34567

# multiple bams in a file(one bam per line)
bam2html -r reference.fa -bl bam.list 1:12345 2:34567

# multiple positions in a file
bam2html -r reference.fa -bl bam.list pos.list

# generate summary.html
bam2html -r reference.fa -bl bam.list pos.list -s

# compress the result
bam2html -r reference.fa -bl bam.list pos.list -s -x zip
bam2html -r reference.fa -bl bam.list pos.list -s -x tar.gz

other optional arguments

• -c/--column: set the width of window
• -color/--color: set the color of highlighted base
• -bg/--background: set the background color of highlighted base
• -o/--prefix: set the prefix of output file
• -O/--outdir: set the output directory