The latest version is Version 0.2
InstallationThe two methods are implemented in the form of two executable JAR files, VST.jar and LRT.jar. The JAR files have no external dependencies, and were tested on Java 1.6 and 1.7, but may run on previous versions. The JARs show usage instructions and command line parameters themselves. To see these, simply run one of the following from your command prompt:
java -jar VST.jar
java -jar LRT.jar
For your convenience, example input files are provided as well. They are:
exampleinput.txt - Contains simulated major and minor allele read counts read counts. Also describes the file format.
exampleci.txt - Contains c_i values, used by LRT method. Also describes the c_i file format.
To run VST and LRT on these examples, assuming a per-base sequencing error rate of 1% (0.01) and with 1000 permutations to obtain a p-value, use the following:
java -jar VST.jar -i exampleinput.txt -e 0.01 -p 1000
java -jar LRT.jar -i exampleinput.txt -e 0.01 -p 1000 -c exampleci.txt -o outputfile.txt -t covariatesfile.txt
Note on large input files: Large input files may require increasing the memory available to the Java Virtual Machine (JVM), by adding the switch -Xmx. If you get OutOfMemory errors, try this: java -Xmx2000m -jar VST.jar ======================================
For further information, please contact the authors of the above article.