For complete details see
http://www.broadinstitute.org/cancer/cga/mutect
And for support please visit
http://gatkforums.broadinstitute.org/categories/mutect
PREREQUISITES
To compile MuTect you must be using Java 1.7 and Ant 1.8. In addition, 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. After building successfully, the MuTect JAR file will be in mutect-src/gatk-protected/dist/packages/muTect-*/muTect.jar
BUILD STEPS
# make a new source directory (e.g. mutect-src)
mkdir mutect-src
cd mutect-src
# get MuTect source
git clone git@github.com:broadinstitute/mutect.git
cd ..
# get the GATK source and set to the latest tested version
git clone git@github.com:broadgsa/gatk-protected.git
cd gatk-protected
git reset --hard 2.7-1-g42d771f
# build
ant -Dexternal.dir=`pwd`/../mutect-src -Dexecutable=mutect package