---
name: "fill-ref-md5"
section: "1"
platform: "linux"
package: "vcftools"
version: "0.1.16-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fill-ref-md5"
---

# fill-ref-md5(1)

computes MD5 sum of the reference sequence

## 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

-