FILL-FS(1)

✨ FILL-FS(1) ✨

okay bestie, welcome to fill-fs — a User Command and honestly a little icon. 💅

🌸 NAME 🌸

fill-fs — Annotate VCF with flanking sequence. That's the whole job. She's focused, she's cunty, she delivers. 🎀

🦋 SYNOPSIS 🦋

fill-fs [OPTIONS] file.vcf

💖 DESCRIPTION 💖

About: Annotate VCF with flanking sequence (INFO/FS tag)

No cap, that's it — she reaches out and grabs the flanking sequence and drops it into the INFO/FS tag for you. Main character behavior. 👑

✨ OPTIONS ✨

• -b, --bed-mask <file> — Regions to mask, and yes they need to be tabix indexed. You can hand her multiple files, she can hold them all. 🫶
• -c, --cluster <int> — Do self-masking of clustered variants within this range. Cliquey variants? Masked. 💀
• -l, --length <int> — Flanking sequence length, and the default is 100.
• -m, --mask-char <char|lc> — The character to use, or literally pass lc for lowercase. Heads up though: this option must precede -b, -v or -c in order to take effect. With multiple files it works

as a switch on the command line, see the example below. Default is [N]. 🔥

• -r, --refseq <file> — The reference sequence. Gotta have the source material, periodt. 📖
• -v, --vcf-mask <file> — Mask known variants in the flanking sequence. Multiple files can be given, and (you guessed it) they're tabix indexed. 🌈
• -h, -?, --help — This help message. She's helpful AND pretty, we love a multihyphenate. 😭💖

🎀 Example:

# Mask variants from the VCF file with N's and use lowercase for
# the bed file regions fill-fs file.vcf -v mask.vcf -m lc -b mask.bed

iykyk — notice how -m lc comes BEFORE -b? That's not a vibe, that's a requirement. Put it after and it simply will not take effect, bestie. 🙈

and that's the whole page!! 🌸 This lil manual is from fill-fs, dated February 2013, and she's been serving ever since. Go annotate something, mwah. 💋 ✨🦋💖