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 Maven 3.0+. After building successfully, the MuTect JAR file will be in mutect/target/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
# 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 3.1
# build the GATK first and install it to the local mvn repo. Once GATK publishes to a public repo this will be much simpler
mvn -Ddisable.queue install
# build MuTect and run unit tests (the target jar will be in target/mutect-*.jar)
cd ../mutect
mvn verify
# run integration tests, if you like
./run_regression.pl
./tieout_regression.pl