#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome Institute at Washington University and is hosted on github. To use Varscan we simply need to download the distributed jar file into our ~/workspace/bin. As with the other java programs which have already been installed in this section we can invoke Varscan via java -jar.
# Install Varscan
cd ~/workspace/bin
curl -L -k -o VarScan.v2.4.2.jar https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar
java -jar ~/workspace/bin/VarScan.v2.4.2.jar
