VCF2GENOMICSDB_INIT(1)

✨ VCF2GENOMICSDB_INIT(1) ✨

okay bestie, sit down, hydrate, and let me tell you about vcf2genomicsdb_init — it's the workspace initializer for GenomicsDB 💖 like it's literally the girl who sets up the whole venue before the party even starts. it's a User Commands page, so it lives in your terminal, and it's here to get your GenomicsDB workspace cute and ready for the vcf import era 🎀

🌸 NAME 🌸

vcf2genomicsdb_init — workspace initializer for GenomicsDB

like. it initializes your workspace. for GenomicsDB. that's the whole vibe 👑

🦋 SYNOPSIS 🦋

vcf2genomicsdb_init [options]

no positional args, just options, and honestly? iconic. she said "flags only, I don't do drama" 💅

✨ OPTIONS ✨

• --help, -h — prints a usage message summarizing all the options available, then dips and exits. your little "wait what do I even do" lifeline 🫶
• --workspace=<GenomicsDB workspace URI>, -w <GenomicsDB workspace URI> — this is the main character option, fr. if the workspace doesn't exist, it gets created first, slay ✨. but if the workspace already exists and you ran this without the overwrite-workspace option? it exits. no cap, she will simply leave 😭
• --overwrite-workspace, -o — gives permission for the workspace json artifacts to be overwritten. use this when you're in your "new era, new jsons" mood 🔥
• --sample-list=<sample list>, -s <sample list file> — tell it which sample URIs to import. one line per sample path, bestie, don't get cute with the formatting 🍓
• --samples-dir=<folder to samples>, -S <folder to samples> — points at a Folder URI that contains your samples. heads up: only vcf.gz/bcf.gz compressed samples are considered. anything else is giving invisible 🫥
• --interval-list=<genomic interval list>, -i <genomic interval list file> — optional! creates array partitions from the intervals in the interval list, one line per interval. the default is to partition by chromosome/contig. also this overrides --number-of-array-partitions and --size-of-array-partitions, so know that before you argue with it 💅
• --number-of-array-partitions=<number>, -n <number> — optional, the suggested number of array partitions. usually the partitioning is per contig. BUT if this is 0, only a single array is created for the entire genomic space, and it overrides all the other partition-specific command arguments. zero is that girl and she knows it 👑
• --size-of-array-partitions=<size>, -z <size> — optional, the suggested size of the array partitions. this one overrides --number-of-array-partitions. size said "I go first" and honestly, valid ✨
• --merge-small-contigs, -m — optional. default is false, and any contig smaller than ~1M gets merged into scaffolds. it's basically "everybody under 1M, get in the group photo" 📸
• --include-fields=<fields>, -f <fields> — optional. only includes the fields (comma-separated, bestie, commas!) listed in this argument while generating the vidmap. the default is to include all fields found in the vcf headers. so if you pass nothing, you get everything, no crumbs left behind 🍓
• --template-loader-json=<template file>, -t <template file> — optional. specifies a template loader json file to use as a basis with the loader json files. think of it as the reference pic you send your stylist 🎀
• --append-samples, -a — optional. if specified, the callsets will be appended with the new samples and lb_row_idx set to the new starting row. note: the workspace and the vidmap/callset/loader jsons should already exist for this. also the interval list, the number and size of partitions, and the merge small contigs options are ignored when you use append samples. she said "those options? not today" 💀
• --verbose, -v — lets verbose messages get logged. for when you want the play-by-play commentary 🎙️✨
• --version — prints the version and exits. short, sweet, no notes 💖

⚠️ real talk bestie: the "workspace already exists" exit and the "these options are ignored with append samples" thing are not decorative. those are facts. read them twice, hydrate, and carry on 🫶

and that's the whole page, periodt 💅 this was vcf2genomicsdb_init from the User Commands collection, dated July 2022, and the footer was repping VCF2GENOMICSDB_INIT(1) — so like, you're in the right manual section, you're doing amazing, go initialize that workspace 🌈👑💖