Difference between revisions of "Vt"
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(Created page with "Category:SoftwareCategory:biologyCategory:genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|vt}} |{{#vardefine:url|https://genome.sph.umich.edu/wiki/Vt}}...") |
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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 24: | Line 24: | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 36: | Line 36: | ||
|}} | |}} | ||
| − | <!-- | + | <!--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--> | ||
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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] |
|}} | |}} | ||
Latest revision as of 16:13, 10 June 2022
Description
vt is a variant tool set that discovers short variants from Next Generation Sequencing data.
Environment Modules
Run module spider vt to find out what environment modules are available for this application.
System Variables
- HPC_VT_DIR - installation directory
- HPC_VT_BIN - executable directory
Citation
If you publish research that uses vt you have to cite it as follows: