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 provides both a C++ API for BAM file support as well as a
 command-line toolkit.
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 This is the bamtools command-line toolkit.
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 Available bamtools commands:
  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)