VCF-PHASED-JOIN(1)

💖 vcf-phased-join(1) 💖

okay so bestie, welcome to vcf-phased-join, a lil User Commands icon that lives in your terminal 🫶

✨ NAME ✨

vcf-phased-join — takes a whole bunch of overlapping pre-phased chunks and squishes them together into one single VCF 💅

🌸 SYNOPSIS 🌸

vcf-phased-join [OPTIONS] A.vcf B.vcf C.vcf

🦋 DESCRIPTION 🦋

About: the script grabs multiple overlapping pre-phased chunks and concatenates them into one VCF. no cap, that's the whole vibe 🎀

and the way it does it?? it uses the heterozygous calls from the overlaps to figure out the correct phase. like, the overlaps are literally doing the detective work for you 🔍✨

💜 OPTIONS 💜

• -j, --min-join-quality <num> — the quality threshold for gluing those pre-phased blocks together. default is 10 🩹
• -l, --list <file> — a list of VCFs to join. giving very much "here's the squad, bring them all" 📋
• -o, --output <file> — the output file name. and when you pass "-", it uses STDOUT and STDERR instead 👑
• -q, --min-PQ <num> — breaks pre-phased segments if the PQ value is lower in the input VCFs. default is 0.6 💔
• -h, -?, --help — this help message. your lil safety net when you forget everything 🙈

ngl bestie, remember those defaults: 10 for join quality and 0.6 for min-PQ. they're just sitting there waiting for you to not pass a flag 🍓

vcf-phased-join 🌈 — the version from February 2013, straight out of the VCF-PHASED-JOIN(1) era. that's the sign-off, mwah 💋✨