Difference between revisions of "BamUtil"

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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*{{#var:app}}
 
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Run-->
 
<!--Run-->
  
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validated 4/5/2018
 

Latest revision as of 17:08, 10 June 2022

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

Environment Modules

Run module spider bamutil to find out what environment modules are available for this application.

System Variables

  • HPC_BAMUTIL_DIR - installation directory