sambamba-slice - copying a slice of BAM file

       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.

sambamba-slice - copying a slice of BAM file

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

                                                   August 2014                                 SAMBAMBA-SLICE(1)

sambambasliceOPTIONS <input.bam> region