VCF2GENOMICSDB(1)

📦 version 1.5.5, in debian bookworm, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 vcf2genomicsdb(1) — the manual, but make it cute 💖

okay bestie, listen up — this is the vcf2genomicsdb page from the User Commands part of the manual, section 1. No cap. Let's get into it. 🦋

🌸 NAME 🌸

vcf2genomicsdb — a VCF data converter for GenomicsDB. it takes your VCF files and, like, moves them into GenomicsDB. that's the whole vibe. ✨

🎀 SYNOPSIS 🎀

vcf2genomicsdb [options] <loader_json_config_file>

so you give it a loader JSON config file (that one's required, bestie, it's not optional) and then however many options your little heart desires. 💅

👑 OPTIONS 👑

here's the full menu. every single one. i would never gatekeep. 🫶

  • --help, -h — you're lost? valid. this shows you the help. 🙈
  • --version — shows the version. iconic, brief, to the point. ⭐
  • --progress, -p — shows the import progress, so you're not just sitting there staring at a silent terminal wondering if it's dead. 😭

you can also tell it the minimum amount of time between progress messages with --progress=<interval> or -p<interval>, where <interval> is a floating point number.

the default units are seconds, but if you want to be specific you can append s, m, or h to the end of the number to explicitly say seconds, minutes, or hours. 💖

  • --tmp-directory, -T — pick your temporary directory. it stores some temporary files during the import process. the default is /tmp. 🍓
  • --rank, -r — manually assign the MPI rank of the process, which determines on which partition the process will operate. main character energy but for a partition. 👑
  • --split-files — splits the files specified by the callset mapping JSON file according to the column partitions in the loader JSON. 🌈

the resulting files will be placed in the same directory as the originals. and the default behavior is to generate split files only for the partition corresponding to the rank. iykyk. ✨

🧚 Modifiers to --split-files 🧚

these are the little add-ons, the accessories to the outfit:

  • --split-all-partitions — overrides the --split-files default behavior and instead creates split files for all partitions. going all in, no half measures. 💅
  • --split-files-results-directory — specify where to place the split files. this overrides the default behavior of placing them in the same directory as the originals. 🎀
  • --split-output-filename — create a split file for one column partition and one VCF. 🦋

e.g.

vcf2genomicsdb <loader.json> --rank=<rank> --split-files --split-output-filename=<output_path> <input.vcf.gz>
  • --split-callset-mapping-file — create callset mapping files containing the paths to the generated split files, one callset per partition. 🌸
heads up bestie: everything above is exactly as the manual says it. i'm just here to make it slay, not to make stuff up. 🔥

and that's the page, fr fr. this one came from vcf2genomicsdb, July 2022, VCF2GENOMICSDB(1) — the User Commands manual. mwah, love u, go convert some VCFs. 💜✨

📦 where this page comes from