Difference between revisions of "BamUtil"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|bamutil}} | |{{#vardefine:app|bamutil}} | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
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Latest revision as of 18:02, 12 August 2022
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
Environment Modules
Run module spider bamutil to find out what environment modules are available for this application.
System Variables
- HPC_BAMUTIL_DIR - installation directory