VarScan: Difference between revisions

Revision as of 16:49, 23 June 2014

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.

Required Modules

Serial

varscan

System Variables

HPC_{{#uppercase:varscan}}_DIR

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>

@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 40: / Line 40: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+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-->