NAME

       bamtools - toolkit for manipulating BAM (genome alignment) files

SYNOPSIS

       bamtools [--help] COMMAND [ARGS]

DESCRIPTION

       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.

OPTIONS

       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.