@BeforeClass private void init() throws IOException { reference = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); dictionary = reference.getSequenceDictionary(); genomeLocParser = new GenomeLocParser(dictionary); header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test"); header.setSequenceDictionary(dictionary); header.setSortOrder(SAMFileHeader.SortOrder.coordinate); readGroup = new GATKSAMReadGroupRecord(header.getReadGroup("test")); final List<GATKSAMRecord> reads = new ArrayList<>(); for (final String contig : contigs) { for (int i = 1; i <= numReadsPerContig; i++) { reads.add(buildSAMRecord("read" + contig + "_" + i, contig, i)); } } createBAM(reads); }