Difference between revisions of "BamUtil"
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Moskalenko (talk | contribs) m (Text replace - "<!--Versions--> ==Available versions== .* <!--Modules-->" to "<!--Modules-->") |
Moskalenko (talk | contribs) m (Text replace - "Usage policy" to "Usage Policy") |
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
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Revision as of 16:29, 10 August 2012
Description
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.