Difference between revisions of "BamUtil"

From UFRC
Jump to navigation Jump to search
m (Text replace - "<!--Versions--> ==Available versions== .* <!--Modules-->" to "<!--Modules-->")
m (Text replacement - "#uppercase" to "uc")
 
(4 intermediate revisions by 2 users not shown)
Line 37: Line 37:
  
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Execution Environment and Modules==
+
==Required Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+
[[Modules|modules documentation]]
 +
===Serial===
 +
*{{#var:app}}
 
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
<!--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
Line 52: Line 57:
 
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)
 
|}}
 
|}}
Line 71: Line 76:
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
 +
=Validation=
 +
* Validated 4/5/2018

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