BamUtil: Difference between revisions
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Moskalenko (talk | contribs) m Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} " |
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[[Category:Software]][[Category: | [[Category:Software]][[Category:Biology]][[Category:Genomics]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|bamutil}} | |{{#vardefine:app|bamutil}} | ||
| Line 35: | Line 35: | ||
Dummy/Example Tools | Dummy/Example Tools | ||
* readReference | * readReference | ||
<!--Modules--> | <!--Modules--> | ||
==Environment Modules== | |||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
==System Variables== | |||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |||
<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | ||
| Line 56: | Line 54: | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
<!--Policy--> | <!--Policy--> | ||
{{#if: {{#var: policy}}|==Usage | {{#if: {{#var: policy}}|==Usage Policy== | ||
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) | ||
|}} | |}} | ||
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