toolkit for manipulating BAM (genome alignment) files


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.

BamTools provides both a C++ API for BAM file support as well as a command-line toolkit.

This is the bamtools command-line toolkit.

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)

Upload more screenshots

Please help extend the collection of screenshots. Just make a screenshot and upload it here. You don't need to register or anything.

Upload a screenshot

Hint: upload an image here from your clipboard with Ctrl-V


Install this software package

If the package is available for the distribution you are currently using on your computer then install the software by clicking on…

Install bamtools