Difference between revisions of "BamUtil"

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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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Dummy/Example Tools
 
Dummy/Example Tools
 
* readReference
 
* readReference
<!--Location-->
+
 
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
<!--Versions-->
 
==Available versions==
 
* 1.0.2
 
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Running the application using modules==
+
==Environment Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+
==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
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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.|}}
 
<!--Policy-->
 
<!--Policy-->
{{#if: {{#var: policy}}|==Usage policy==
+
{{#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 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