public void initialize() {
samples =
SampleUtils.getSampleListWithVCFHeader(
getToolkit(), Arrays.asList(variantCollection.variants.getName()));
beagleWriter.print("marker alleleA alleleB");
for (String sample : samples)
beagleWriter.print(String.format(" %s %s %s", sample, sample, sample));
beagleWriter.println();
if (bootstrapVCFOutput != null) {
initializeVcfWriter();
}
if (VQSRCalibrationFile != null) {
VQSRCalibrator = VQSRCalibrationCurve.readFromFile(VQSRCalibrationFile);
logger.info("Read calibration curve");
VQSRCalibrator.printInfo(logger);
}
}
