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[ Source: bamtools  ]

Package: bamtools (2.3.0+dfsg-2)

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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)

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Architecture Package Size Installed Size Files
amd64 177.4 kB627.0 kB [list of files]
armel 149.8 kB538.0 kB [list of files]
armhf 154.0 kB434.0 kB [list of files]
i386 179.0 kB617.0 kB [list of files]