Paquet : bamtools (2.5.1+dfsg-10build1)

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)