NAME

       sambamba-index - 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

                                            2016-10-24                          SAMBAMBA-INDEX(1)