Man page - fill-ref-md5(1)
Packages contas this manual
- vcf-subset(1)
- vcf-merge(1)
- vcf-compare(1)
- vcf-to-tab(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-contrast(1)
- vcf-isec(1)
- vcf-validator(1)
- fill-ref-md5(1)
- vcf-convert(1)
- vcf-annotate(1)
- vcf-concat(1)
- fill-an-ac(1)
- vcf-fix-newlines(1)
- vcf-query(1)
- vcf-stats(1)
- vcf-consensus(1)
- vcf-tstv(1)
- fill-aa(1)
- vcf-phased-join(1)
- fill-fs(1)
- vcf-shuffle-cols(1)
- vcftools(1)
- vcf-fix-ploidy(1)
Package: vcftools
apt-get install vcftools
apt-get install vcftools
Manuals in package:
Documentations in package:
Manual
| FILL-REF-MD5(1) | User Commands | FILL-REF-MD5(1) |
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
| February 2013 | fill-ref-md5 |