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
- validate, diff, stats, gapInfo
Tools to Print Information In Readable Format
- dumpHeader, dumpRefInfo, dumpIndex, 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.