Difference between revisions of "BamUtil"
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Moskalenko (talk | contribs) m (Text replace - "Usage policy" to "Usage Policy") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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<!--Modules--> | <!--Modules--> | ||
| − | + | ==Required Modules== | |
| − | + | [[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 | ||
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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 | ||
Revision as of 21:13, 6 December 2019
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
Required Modules
Serial
- bamutil
System Variables
- HPC_BAMUTIL_DIR - installation directory
Validation
- Validated 4/5/2018