VCF-MERGE(1)

💖 NAME 💖

vcf-merge — bestie, this is the girl that merges your bgzipped and tabix indexed VCF files ✨

🌸 SYNOPSIS 🌸

merge-vcf [OPTIONS] file1.vcf file2.vcf.gz ... > out.vcf

🦋 DESCRIPTION 🦋

okay so About: vcf-merge merges the bgzipped and tabix indexed VCF files. and yes she needs them both bgzipped and tabix indexed, no shortcuts, no exceptions 🎀 — like literally, do this first:

bgzip file.vcf; tabix -p vcf file.vcf.gz

that's the whole vibe. index your files, then let her cook 🔥

✨ OPTIONS ✨

• -c, --chromosomes <list|file> — Same as -r, left for backward compatibility. > Please do not use as it will be dropped in the future. it's giving deprecated legacy energy, bestie, she's on her way out 💀
• -d, --remove-duplicates — If there should be two consecutive rows with the same chr:pos, print only the first one. one row per spot, we don't do repeats here 💅
• -H, --vcf-header <file> — Use the VCF header. yes queen, bring your own header 👑
• -h, -?, --help — This help message. when in doubt, ask the girl directly 🫶
• -r, --regions <list|file> — Do only the given regions (comma-separated list or one region per line in a file). pick your faves, she'll only serve those ⭐
• -s, --silent — Try to be a bit more silent, no warnings about duplicate lines. not me turning off the duplicate-line warnings because the chat was too loud 🙈

fr fr: -c is the same as -r but do not use it, it's getting dropped later. use -r, she's the main character 💖

and that's the whole page, babe 🧚 this was the vcf-merge manual from vcf-merge 0.1.5, dated July 2011, filed under User Commands — tysm for reading, ily, go index your VCFs 🌈💜