fill-ref-md5 - computes MD5 sum of the reference sequence

       About: The script computes MD5 sum of the reference sequence and inserts

              'reference'  and  'contig'  tags  into  header  as  recommended  by VCFv4.1.  The VCF file must be
              compressed and tabix indexed,  as  it  takes  advantage  of  the  lightning  fast  tabix  reheader
              functionality.

       fill-ref-md5 -i AS:NCBIM37,SP:"Mus\ Musculus" -r NCBIM37_um.fa
              -d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz

fill-ref-md5                                      February 2013                                  FILL-REF-MD5(1)

       fill-ref-md5 - computes MD5 sum of the reference sequence

-d, --dictionary <file>
              Where to read/write computed MD5s. Opened in append mode, existing records are not touched.

       -i, --info <AS:xx,SP:xx,TX:xx>
              Optional info on reference assembly (AS), species (SP), taxonomy (TX)

       -r, --refseq <file>
              The reference sequence in fasta format indexed by samtools faidx

       -h, -?, --help
              This help message.

fill-ref-md5 [OPTIONS] in.vcf.gzout.vcf.gz