This is the command fill-ref-md5 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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