BamUtil

Description

bamutil website  

Programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

Tools to Rewrite SAM/BAM Files:

• convert, writeRegion, splitChromosome, splitBam, trimBam, rgMergeBam, polishBam, findCigars.

Tools to Modify & write SAM/BAM Files:

• clipOverlap, filter, revert, squeeze

Informational Tools:

• validate, diff, stats, gapInfo

Tools to Print Information In Readable Format

• dumpHeader, dumpRefInfo, dumpIndex, readReference

Additional Tools

• bam2FastQ

Dummy/Example Tools

• readReference

Execution Environment and Modules

To use bamutil with the environment modules system at HPC the following commands are available:

Get module information for bamutil:

$module spider bamutil

Load the default application module:

$module load bamutil

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_BAMUTIL_DIR - directory where bamutil is located.