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BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.


Free to use and open source under MIT License


  • Puhti: 2.5.1
  • Chipster graphical user interface


In Puhti, Bamtools can be taken in use as a part of biokit module collection:

module load biokit
The biokit modules sets up a set of commonly used bioinformatics tools. Note however that there are bioinformatics tools in Puhti, that have a separate setup commands.

The syntax of bamtools is:

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)

For more information on a specific command, run command:

bamtools help COMMAND



More information about Bamtoos can be found from the Bamtools home page.

Last update: October 10, 2022