How do I build ContEst from the source?
ContEst is implemented as an external walker for the GATK. In order to build ContEst, you should first be able to build the GATK source. Instructions for building the GATK can be found here
In addition, it is necessary to download the Apache BCEL Library and put it in either your system classpath, or your Ant installation lib directory.
Next, download the ContEst source bundle. For this example, it is assumed that you have unpackaged the bundle into /home/contest and that the GATK source is in /home/gatk.
From the GATK build directory, run:
ant -Dexternal.dir=/home/contest -Dexecutable=contest package
After a successful build, the ContEst.jar can be found under /home/gatk/dist/packages/ContEst*/ContEst.jar