NAME

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

SYNOPSIS

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

DESCRIPTION

       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.

OPTIONS

       -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.

EXAMPLES

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