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[sambamba index] documentation
lomereiter edited this page Aug 9, 2012
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sambamba-index - tool for building standard index files for BAM data
sambamba-index [-p|--show-progress] <input.bam> [<output.bai>]
sambamba-index builds an index for a sorted by coordinate BAM file.
This step is required for effective region querying in most tools for working
with BAM data.
An index is by default written to the file with the same filename except
.bai extension added to the end. The user can, however, override this default
by providing desired output filename explicitly as an optional command-line
argument.
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-p,--show-progress - Show a wget-like progressbar in STDERR.
Build index file example.bam.bai given a sorted BAM file example.bam:
$ sambamba-index example.bam
Build index file at custom location showing progress:
$ sambamba-index --show-progress example.bam /tmp/example.bam.bai