VCF files can contain annotations of single nucleotide variants, insertions/deletions, copy number variants, structural variants or other types of genomic variation. They must be compressed and indexed using tabix (http://sourceforge.net/projects/samtools/files/tabix/). Like BAM index files, the separate tabix-formatted .tbi index file must be included in the same directory as the compressed VCF file and must have the same root file name.
