Difference between revisions of "Vt"
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Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|vt}} | |{{#vardefine:app|vt}} | ||
| − | |{{#vardefine:url| | + | |{{#vardefine:url|http://genome.sph.umich.edu/wiki/Vt}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | ||
| − | |{{#vardefine: | + | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> |
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
| Line 21: | Line 21: | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Required Modules== |
| − | + | ||
| + | ===Serial=== | ||
| + | * {{#var:app}} | ||
| + | <!-- | ||
| + | ===Parallel (OpenMP)=== | ||
| + | * intel | ||
| + | * {{#var:app}} | ||
| + | ===Parallel (MPI)=== | ||
| + | * intel | ||
| + | * openmpi | ||
| + | * {{#var:app}} | ||
| + | --> | ||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| − | |||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 36: | Line 46: | ||
|}} | |}} | ||
| − | <!-- | + | <!--PBS scripts--> |
| − | {{#if: {{#var: | + | {{#if: {{#var: pbs}}|==PBS Script Examples== |
| − | See the [[{{PAGENAME}} | + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples. |
|}} | |}} | ||
<!--Policy--> | <!--Policy--> | ||
| Line 59: | Line 69: | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. Unified Representation of Genetic Variants. Bioinformatics (2015) 31(13): 2202-2204 | + | [http://bioinformatics.oxfordjournals.org/content/31/13/2202 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. Unified Representation of Genetic Variants. Bioinformatics (2015) 31(13): 2202-2204] |
|}} | |}} | ||
Revision as of 20:01, 27 May 2022
Description
vt is a variant tool set that discovers short variants from Next Generation Sequencing data.
Required Modules
Serial
- vt
System Variables
- HPC_VT_DIR - installation directory
Citation
If you publish research that uses vt you have to cite it as follows: