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How to build MuTect


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


# make a new source directory (e.g. mutect-src)
mkdir mutect-src
cd mutect-src

# get MuTect source
git clone

# get the GATK source and set to the latest tested version
git clone
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