if ( verboseWriter != null )
verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tMLE\tMAP");
final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
final AFCalculatorProvider afCalcAFCalculatorProvider = FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),UAC,logger);
genotypingEngine = new UnifiedGenotypingEngine(UAC, samples, toolkit.getGenomeLocParser(), afCalcAFCalculatorProvider, toolkit.getArguments().BAQMode);
genotypingEngine.setVerboseWriter(verboseWriter);
genotypingEngine.setAnnotationEngine(annotationEngine);
// initialize the header