github.com/broadinstitute/mutect @1.1.6

Overview

For complete details see

http://www.broadinstitute.org/cancer/cga/mutect

And for support please visit

http://gatkforums.broadinstitute.org/categories/mutect

How to build 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