Provided by: vcftools_0.1.15-1_amd64 
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