bamtools - toolkit for manipulating BAM (genome alignment) files

       BamTools  facilitates  research analysis and data management using BAM files.  It copes with the enormous
       amount of data produced by current sequencing technologies that is typically stored in compressed, binary
       formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.

       bamtools - toolkit for manipulating BAM (genome alignment) files

       convert
              Converts between BAM and a number of other formats

       count  Prints number of alignments in BAM file(s)

       coverage
              Prints coverage statistics from the input BAM file

       filter Filters BAM file(s) by user-specified criteria

       header Prints BAM header information

       index  Generates index for BAM file

       merge  Merge multiple BAM files into single file

       random Select random alignments from existing BAM file(s), intended more as a testing tool.

       resolve
              Resolves paired-end reads (marking the IsProperPair flag as needed)

       revert Removes duplicate marks and restores original base qualities

       sort   Sorts the BAM file according to some criteria

       split  Splits a BAM file on user-specified property, creating a new BAM output file for each value found

       stats  Prints some basic statistics from input BAM file(s)

       See 'bamtools help COMMAND' for more information on a specific command.

bamtools 2.3.0+dfsg                                April 2014                                        BAMTOOLS(1)

bamtools [--help] COMMAND [ARGS]