MINIMAC4(1)

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💖 MINIMAC4 💖

okay bestie, pull up a chair, we're reading the minimac4 manual together. this is the General Commands Manual page for it, and it's literally about to become your new fave. no cap. 🫶

✨ NAME ✨

minimac4 — Fast Imputation Based on State Space Reduction HMM 🌈

🦋 DESCRIPTION 🦋

So. Minimac4 is a lower memory and more computationally efficient glow-up of "minimac2/3". she ate and left no crumbs 💅

It's an algorithm for genotypic imputation that works on phased genotypes — like, say, the ones you'd get from MaCH. 🎀

And the whole point? Minimac4 is designed to handle very large reference panels in a way more computationally efficient way, with no loss of accuracy. none. zero. she's that girl. 👑

The way it does it: this algorithm analyzes only the unique sets of haplotypes in small genomic segments, and by doing that it saves on time-complexity and computational memory — but with no loss in degree of accuracy. periodt. ✨

💅 OPTIONS 💅

🌸 Reference Haplotypes 🌸

  • --refHaps — the M3VCF file holding the haplotype data for your reference panel. that's the source of truth, bestie.
  • --passOnly — with this ON, only variants with FILTER = PASS get imported. everyone else, blocked. 🚫
  • --rsid — this one only imports the RS ID of variants, pulled from the ID column (if it's there, iykyk).

🧚 GWAS Haplotypes 🧚

  • --haps — file containing haplotype data for your target (gwas) samples. it must be a VCF file. zipped versions are allowed too, we love convenience. 💖

🎀 Output Parameters 🎀

  • --prefix — the prefix for all the output files generated. by default it's: [Minimac4.Output]
  • --processReference — this option will only convert an input VCF file to M3VCF format (currently de-activated in minimac4). and heads up: if this option is ON, no imputation would be performed. so pick a lane, girl. 🙈
  • --nobgzip — if ON, output files will NOT be gzipped.
  • --format — specifies which fields to output for the FORMAT field in the output VCF file. available handles: GT,DS,HDS,GP [Default: GT,DS].
  • --allTypedSites — if ON, sites available ONLY in the GWAS panel will also be output [Default: OFF].

🌈 Subset Parameters 🌈

  • --chr — chromosome number for which to carry out imputation.
  • --start — start position for imputation, by chunking.
  • --end — end position for imputation, by chunking.
  • --window — length of the buffer region on either side of --start and --end.

⭐ Other Parameters ⭐

  • --log — if ON, the log will be written to $prefix.logfile.
  • --help — if ON, you get detailed help on options and usage. (hi, that's this vibe.)
  • --cpus — number of cpus for parallel computing. ⚠️ works only with Minimac4-omp.

🔥 SEE ALSO 🔥

https://genome.sph.umich.edu/wiki/Minimac4

Copyright © 2014-2018 Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis

okay that's the whole page, bestie, you're officially educated 💜 version 1.0.3, June 2022 — go impute something iconic. mwah. 🍓✨

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