VarScan: Difference between revisions
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Moskalenko (talk | contribs) Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|varscan}} |{{#vardefine:url|http://varscan.sourceforge.net/..." |
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[[Category:Software]][[Category: | [[Category:Software]][[Category:Biology]][[Category:NGS]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|varscan}} | |{{#vardefine:app|varscan}} | ||
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<!--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|1}} <!--ADDITIONAL INFO--> | ||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina HiSeq2000 yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing (NGS) platforms presents a substantial informatics challenge. VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data. | The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina HiSeq2000 yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing (NGS) platforms presents a substantial informatics challenge. VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data. | ||
<!--Modules--> | <!--Modules--> | ||
== | ==Environment Modules== | ||
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 | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
VarScan software is contained in a platform-independent Java .jar file. Therefore, to run it call java as | |||
java -Xmx<SIZE>g -jar $HPC_VARSCAN_DIR/VarScan.jar <command> <arguments> | |||
or use the wrapper script we provide as | |||
VarScan -Xmx<SIZE>g <command> <arguments> | |||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
Latest revision as of 20:54, 12 August 2022
Description
The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina HiSeq2000 yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing (NGS) platforms presents a substantial informatics challenge. VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.
Environment Modules
Run module spider varscan to find out what environment modules are available for this application.
System Variables
- HPC_VARSCAN_DIR - installation directory
Additional Information
VarScan software is contained in a platform-independent Java .jar file. Therefore, to run it call java as
java -Xmx<SIZE>g -jar $HPC_VARSCAN_DIR/VarScan.jar <command> <arguments>
or use the wrapper script we provide as
VarScan -Xmx<SIZE>g <command> <arguments>