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Command line tools
lomereiter edited this page Jun 21, 2012
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There's a command line tool Sambamba, built on top of the library, located in CLItools/
directory. For compilation you need either DMD compiler (install from repository of download from http://dlang.org/download.html) or GDC (install according to instructions on https://bitbucket.org/goshawk/gdc/wiki/Home)
Usage: sambamba [options] <input.bam> [region1 [...]]
Options: -q, --quality-threshold=THRESHOLD
skip reads with mapping quality < THRESHOLD
-r, --read-group=READGROUP
output only reads from read group READGROUP
-f, --format=sam|json
specify which format to use for output (default is SAM)
-h, --with-header
print header before reads
-H, --header
output only header
-I, --reference-info
output only reference names and lengths in JSON
-c, --count
output only count of matching records, hHI are ignored
Regions are specified as in samtools, e.g. "chr1:1,000-2000" or "chr2" or "chr3:1,000,000". The tool outputs reads in SAM format by default, but you can also specify JSON.
cd CLItools/
make sambamba-dmd
The executable sambamba
will be in CLItools/build
directory. You can just copy it to /usr/local/bin
.