Difference between revisions of "BamUtil"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|bamutil}} |{{#vardefine:url|http://genome.sph.umich.edu/wiki/B...") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
| + | |||
Programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. | Programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. | ||
| Line 34: | Line 35: | ||
Dummy/Example Tools | Dummy/Example Tools | ||
* readReference | * readReference | ||
| − | + | ||
| − | |||
| − | |||
| − | |||
| − | |||
<!--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}}_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 | + | {{#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) | ||
|}} | |}} | ||
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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