Set<VCFHeaderLine> headerInfo = getHeaderInfo(UAC, annotationEngine, dbsnp);
headerInfo.addAll(genotypingEngine.getAppropriateVCFInfoHeaders());
// invoke initialize() method on each of the annotation classes, allowing them to add their own header lines
// and perform any necessary initialization/validation steps
annotationEngine.invokeAnnotationInitializationMethods(headerInfo);
final Set<String> samplesForHeader;
if ( ! onlyEmitSamples.isEmpty() ) {
// make sure that onlyEmitSamples is a subset of samples
if ( ! sampleNameSet.containsAll(onlyEmitSamples) )