.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.1.
.TH FILL-REF-MD5 "1" "February 2013" "fill-ref-md5" "User Commands"
.SH NAME
fill-ref-md5 \- computes MD5 sum of the reference sequence
.SH SYNOPSIS
.B fill-ref-md5
[\fIOPTIONS\fR] \fIin.vcf.gz out.vcf.gz\fR
.SH DESCRIPTION
About: The script computes MD5 sum of the reference sequence and inserts
.IP
\&'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.
.SH OPTIONS
.TP
\fB\-d\fR, \fB\-\-dictionary\fR <file>
Where to read/write computed MD5s. Opened in append mode, existing records are not touched.
.TP
\fB\-i\fR, \fB\-\-info\fR <AS:xx,SP:xx,TX:xx>
Optional info on reference assembly (AS), species (SP), taxonomy (TX)
.TP
\fB\-r\fR, \fB\-\-refseq\fR <file>
The reference sequence in fasta format indexed by samtools faidx
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SH EXAMPLES
.TP
fill\-ref\-md5 \-i AS:NCBIM37,SP:"Mus\e Musculus" \-r NCBIM37_um.fa
\-d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz
.IP