//static member function - set number of threads
PairHMM.setNumberOfThreads(getToolkit().getTotalNumberOfThreads());
// create our likelihood calculation engine
likelihoodCalculationEngine = createLikelihoodCalculationEngine();
final MergeVariantsAcrossHaplotypes variantMerger = mergeVariantsViaLD ? new LDMerger(SCAC.DEBUG, 10, 1) : new MergeVariantsAcrossHaplotypes();
genotypingEngine.setCrossHaplotypeEventMerger(variantMerger);
genotypingEngine.setAnnotationEngine(annotationEngine);