BamTools

Introduction

BamTools provides a small, but powerful suite of command-line utility programs for manipulating and querying BAM files for data.

Available bamtools commands are:

• 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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Installed version

The currently installed version is 2.4.0.

Using BamTools with the HPC Cluster

If you want to find out more about BEDtools on the HPC Cluster, you can use the command

module spider bamtools

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command

module load BamTools/2.4.0-intel-2016b

Always remember: this command is case sensitive!

After loading the module, you can use the program with

bamtools <COMMAND> [ARGS]

Documentation

Further Information can be found on the project website.