Difference between revisions of "BamUtil"

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m (Text replacement - "#uppercase" to "uc")
 
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<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Run-->
 
<!--Run-->
  

Latest revision as of 21:13, 6 December 2019

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

Required Modules

modules documentation

Serial

  • bamutil

System Variables

  • HPC_BAMUTIL_DIR - installation directory






Validation

  • Validated 4/5/2018