BamUtil

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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






Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=BamUtil&oldid=24716"