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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