From HPC wiki


BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files. bamtools v2.3.0 is installed across all HPC nodes.


bamtools can be loaded as a module:

[asrini@node062 ~]$ module show bamtools-2.3.0

module-whatis	 BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
prepend-path	 PATH /opt/software/bamtools/2.3.0/bin
prepend-path	 LD_LIBRARY_PATH /usr/lib64:/usr/lib:/usr/local/lib:/opt/software/bamtools/2.3.0/lib/

[asrini@node062 ~]$ module load bamtools-2.3.0

[asrini@node062 ~]$ which bamtools

[asrini@node062 ~]$ bamtools

usage: bamtools [--help] COMMAND [ARGS]

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)

See 'bamtools help COMMAND' for more information on a specific command.

Other Pages