NAME

       sambamba-slice - copying a slice of BAM file

SYNOPSIS

       sambamba slice OPTIONS <input.bam> region

DESCRIPTION

       Outputs  reads  overlapping  specified  region  into new BAM file. (Default destination is
       STDOUT.) Input file must be coordinate-sorted and indexed.

       While the same can be done with sambamba-view, that would be much slower due to a  lot  of
       compression/decompression   work.   Instead  of  naive  method,  sambamba-slice  leverages
       knowledge about structure of BAM file and recompresses only  a  few  BGZF  blocks  at  the
       beginning and the end of the region, while the BGZF blocks in the middle are copied as is.
       As such, this tool doesn´t offer any options related to number of threads  or  compression
       level - most of the time is spent on I/O operations.

OPTIONS

       -o, --output-filename=OUTPUTFILE
              Name of output file

                                           August 2014                          SAMBAMBA-SLICE(1)