BamTools

The SAM/BAM format is a standard format for short read alignments. While SAM is the plain-text version of the alignments, BAM is compressed, binary format of the alignments that is used for space-saving. BamTools is a toolkit for handling BAM files. BamTools provides a powerful suite of command-lines programs for manipulating and querying BAM files for data.

The basic usage of BamTools is:

$ bamtools COMMAND [options]

• 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)

For detailed description and more information on a specific command, just type:

$ bamtools help COMMAND

The page Running BamTools Commands shows how to run BamTools on HCC.