VCFFileReader file= new VCFFileReader(file.vcf, file.vcf.gz.tbi, true)
to open a file and then
CloseableIterator<VariantContext> vc = file.query("10", 77162995, 131048262)
to query specific regions of the file. The problem is that when I choose a region in the middle or the end of the chromosome the method doesn't return anything. For the region starting at position 77162995 and end at 131048262 it doesn't work.