FILL-REF-MD5(1)

💖 FILL-REF-MD5 💖

okay so bestie, lemme put you onto fill-ref-md5, a lil User Commands icon from the FILL-REF-MD5(1) manual. she's lowkey a genius and highkey underrated, and by the end of this you're gonna be obsessed. periodt. ✨

✨ 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, because the whole point is that it takes advantage of the lightning fast tabix reheader functionality. ⚡ like, no cap, it's giving speed. 🏎️💨

🎀 OPTIONS 🎀

• -d, --dictionary <file> — where to read/write computed MD5s. opened in append mode, so existing records are not touched. respectful queen behavior, she minds her business. 🙈
• -i, --info <AS:xx,SP:xx,TX:xx> — optional info on reference assembly (AS), species (SP), taxonomy (TX). optional bestie, no pressure. 💜
• -r, --refseq <file> — the reference sequence in fasta format indexed by samtools faidx. yes you gotta index it first, she's not doing that part for you. 😭
• -h, -?, --help — this help message. the classic. the icon. 💅

🌈 EXAMPLES 🌈

okay here's the moment you've been waiting for, the main character example:

fill-ref-md5 -i AS:NCBIM37,SP:"Mus\ Musculus" -r NCBIM37_um.fa
      -d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz

look at her go. 🫶 -i feeding in the assembly/species/taxonomy info, -r pointing at the indexed fasta, -d writing the dictionary, and in.vcf.gz ➡️ out.vcf.gz doing the actual glow-up. ate, honestly. ⭐

ngl bestie, don't forget that in.vcf.gz has to be compressed and tabix indexed or this whole vibe check fails. 🚨

and that's the tea! 🍓 this page was brought to you by fill-ref-md5 herself, straight outta February 2013, documented in the FILL-REF-MD5(1) manual. go forth and tag those headers, queen. 👑💖