Sambamba documentation

NAME

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

SYNOPSIS

sambamba index [-p|--show-progress] [-n|--threads=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