Changes

     vcf-file    VCF file (can be gzipped or bgzipped)

     vcf-file    VCF file (can be gzipped or bgzipped)

     g              genome-file (Memory Mapped Sequence file)  

     g              genome-file (fasta file)  

                   (note that if genome.fa is specified, the actual file looked for is genome-bs.umfa)

                   (note that if genome.fa is specified, the actual file looked  

                    for is genome-bs.umfa, if the memory mapped file is not

                    found, it will be automatically generated from the fasta file)

     s              statistical analysis

     s              statistical analysis

     a              annotation

     a              annotation