VCF-CONTRAST(1)

🦋 NAME 🦋

vcf-contrast — the little icon that finds differences amongst samples 💅✨

🌸 SYNOPSIS 🌸

vcf-contrast +<list> -<list> [OPTIONS] file.vcf.gz

✨ DESCRIPTION ✨

okay bestie so here's the tea ☕ — About: this one finds differences amongst samples and then drops a NOVEL* annotation into the INFO field. that's literally it, that's the whole vibe 💖

🎀 OPTIONS 🎀

• +<list> — the list of samples where a unique variant is expected 👑 these are your main characters.
• -<list> — the list of background samples 🫶 the supporting cast, the control group, the ones who are just there being normal.
• -d, --min-DP <int> — minimum depth across all the -<list> samples. like, if the depth isn't there, we're not doing this 🙈
• -f, --apply-filters — skips sites whose FILTER column is anything other than PASS or "." 💀 strict queen behaviour, honestly.
• -n, --novel-sites — prints only the records with novel genotypes. no filler, just the good stuff ✨
• -h, -?, --help — this help message 🥰 hi bestie, you're doing great.

🌈 Example:

# Test if any of the samples A,B is different from all C,D,E
vcf-contrast +A,B -C,D,E -m file.vcf.gz

# Same as above but printing only sites with novel variants and table output
vcf-contrast -n +A,B -C,D,E -m file.vcf.gz | vcf-query -f '%CHROM
%POS\t%INFO/NOVELTY\t%INFO/NOVELAL\t%INFO/NOVELGT[\t%SAMPLE %GTR %PL]\n'

# Similar to above but require minimum mapping quality of 20
vcf-annotate -f MinMQ=20 file.vcf.gz | vcf-contrast +A,B,C -D,E,F -f

and that's the whole page, bestie 🧚 no cap, you're basically a bioinformatician now 💜

this was brought to you by vcf-contrast, February 2013 vintage 🍓 — stay slay, stay filtered, stay novel 👑💖