@@ -0,0 +1,769 @@
+package com.github.sparkcaller.variantdiscovery;%0A%0Aimport com.github.sparkcaller.BaseGATKProgram;%0Aimport org.broadinstitute.gatk.engine.CommandLineGATK;%0A%0Aimport java.io.File;%0Aimport java.util.ArrayList;%0Aimport java.util.List;%0A%0Apublic class GenotypeGVCF extends BaseGATKProgram %7B%0A%0A    public GenotypeGVCF(String pathToReference, String extraArgs) %7B%0A        super(%22GenotypeGVCFs%22, extraArgs);%0A        setReference(pathToReference);%0A    %7D%0A%0A    public File performJointGenotyping(List%3CFile%3E vcfFilenames, String outputFilename) throws Exception %7B%0A        for (File vcfFile : vcfFilenames) %7B%0A            addArgument(%22--variant%22, vcfFile.getPath());%0A        %7D%0A%0A        setOutputFile(outputFilename);%0A        executeProgram();%0A%0A        return new File(outputFilename);%0A    %7D%0A%7D%0A

Create the class which will be used when performing joint genotyping.