Difference between revisions of "VarScan"

Jump to navigation Jump to search
Line 71: Line 71:
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
* Validated 4/5/2018

Revision as of 18:53, 5 April 2018


varscan website  

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


  • 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>


  • Validated 4/5/2018