BamTools

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

• BamTools
  • License
  • Available
  • Usage
  • Support
  • More information

License

Free to use and open source under the MIT License.

Available

• Roihu-CPU: 2.5.2, via the bio-apps module.

Usage

BamTools is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the BamTools module:

module load bio-apps/v202603
module load bamtools/2.5.2

Check the available versions with:

module spider bamtools

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:

bamtools help COMMAND

Support

CSC Service Desk

More information

• BamTools home page

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