sambamba-index - tool for building standard index files for BAM data

sambambaindex  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.

       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

sambamba-index - tool for building standard index files for BAM data

-p, --show-progress
              Show a wget-like progressbar in STDERR.

       -t, --nthreads=NTHREADS
              Number of threads to use.

       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)

sambambaindex [-p|--show-progress] [-t|--nthreads=NTHREADS] <input.bam> [<output.bai>]