HPC:bamtools
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bamtools
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.
Usage
bamtools can be loaded as a module:
[asrini@node062 ~]$ module show bamtools-2.3.0 ------------------------------------------------------------------- /usr/share/Modules/modulefiles/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 /opt/software/bamtools/2.3.0/bin/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.
