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sambamba-index(1) -- tool for building standard index files for BAM data
========================================================================
## SYNOPSIS
`sambamba index` [`-p`|`--show-progress`] [`-t`|`--nthreads`=NTHREADS] <input.bam> [<output.bai>]
## DESCRIPTION
`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.
## OPTIONS
* `-p`, `--show-progress`:
Show a wget-like progressbar in STDERR.
* `-t`, `--nthreads`=<NTHREADS>:
Number of threads to use.
## EXAMPLES
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
## SEE ALSO
For more information on the original samtools INDEX behaviour, check
out the [samtools documentation](http://samtools.sourceforge.net/samtools.shtml)
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