bcfWriter.writeHeader(vcfFile.getFileHeader()); for (VariantContext vc : vcfFile.iterator().toList()) { Assert.assertEquals(vc.getGenotypes().stream().filter(Genotype::isPhased).count(), 2); bcfWriter.add(vc); for (VariantContext vc : vcfOutput.iterator().toList()) { Assert.assertEquals(vc.getGenotypes().stream().filter(Genotype::isPhased).count(), 2);