View source for BamUtil

[[Category:Software]][[Category:Biology]][[Category:Genomics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|bamutil}}
|{{#vardefine:url|http://genome.sph.umich.edu/wiki/BamUtil}}
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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

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==Environment Modules==
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==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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{{#if: {{#var: exe}}|==How To Run==
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{{#if: {{#var: conf}}|==Configuration==
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*'''Q:''' **'''A:'''|}}
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