Skip to content

Docs CSC now features an automatic Finnish translation. Click here for more information.

Warning!

Puhti and Mahti will be decommissioned after Roihu becomes available. Users should clean up unnecessary files and move any required data by the end of August 2026. See the Roihu data preparation instructions for details.

Puhti scratch is very full: keep only active data there and move or delete everything else. No new Puhti scratch quota will be granted.

BamTools

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

License

Free to use and open source under MIT License

Available

  • Puhti: 2.5.2
  • Chipster graphical user interface

Usage

On Puhti, BamTools can be taken in use as a part of biokit module collection:

module load biokit

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

The syntax of BamTools is:

bamtools COMMAND ARGUMENTS

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

Support

CSC Service Desk

More information

More information about BamTools can be found from the BamTools home page.