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BAMTOOLS(1) User Commands BAMTOOLS(1)


bamtools - toolkit for manipulating BAM (genome alignment) files


bamtools [--help] COMMAND [ARGS]


BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.


Converts between BAM and a number of other formats
Prints number of alignments in BAM file(s)
Prints coverage statistics from the input BAM file
Filters BAM file(s) by user-specified criteria
Prints BAM header information
Generates index for BAM file
Merge multiple BAM files into single file
Select random alignments from existing BAM file(s), intended more as a testing tool.
Resolves paired-end reads (marking the IsProperPair flag as needed)
Removes duplicate marks and restores original base qualities
Sorts the BAM file according to some criteria
Splits a BAM file on user-specified property, creating a new BAM output file for each value found
Prints some basic statistics from input BAM file(s)

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

April 2014 bamtools 2.3.0+dfsg