@@ -0,0 +1,711 @@
+package com.github.sparkcaller.variantdiscovery;%0A%0Aimport com.github.sparkcaller.BaseGATKProgram;%0Aimport com.github.sparkcaller.Utils;%0A%0Apublic class RecalibrateVariants extends BaseGATKProgram %7B%0A%0A    public RecalibrateVariants(String pathToReference, String extraArgs) %7B%0A        super(%22VariantRecalibrator%22, extraArgs);%0A        setReference(pathToReference);%0A    %7D%0A%0A    public void recalibrateVariants(String pathToVcf) throws Exception %7B%0A        addArgument(%22-input%22, pathToVcf);%0A        addArgument(%22-recalFile%22, Utils.removeExtenstion(pathToVcf, %22vcf%22) + %22-recal.recal%22);%0A        addArgument(%22-tranchesFile%22, Utils.removeExtenstion(pathToVcf, %22vcf%22) + %22-tranches.tranches%22);%0A%0A        executeProgram();%0A   %7D%0A%7D%0A

Create the class which will be used to obtain the targets which requires variant recalibration.