GMER_CALLER(1)

📦 version 4.0+git20221122.71e6625, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 GMER_CALLER(1) 💖

okay bestie, welcome to the GenomeTester User Manuals and today's main character is gmer_caller — she's the one who shows up after the k-mers have been counted and goes "alright, let's figure out what genotypes these actually ARE." 🧬✨

✨ NAME ✨

gmer_caller — call the genotypes from a file with counted k-mers

like. that's the whole job. counted k-mers go in, genotypes come out. slay. 💅

🌸 SYNOPSIS 🌸

gmer_caller [OPTIONS] <COUNTS_FILE>

so you give her a <COUNTS_FILE> (the counted k-mers, obviously) and however many [OPTIONS] you're feeling, and she does her thing. 🦋

🎀 OPTIONS 🎀

one bullet per flag, no skipping, we're doing this properly:

  • --training_size NUM — use NUM markers for training (default is 100000). that's a lot of markers, she's thorough 💅
  • --runs NUMBER — do NUMBER runs of model training (pass 0 if you want no training at all, like a little rebel)
  • --num_threads NUM — use NUM threads. min 1, max 32, default 16. so many cores, so little time 🔥
  • --header — print the table header. yes queen, label your columns 👑
  • --non_canonical — output non-canonical genotypes. we're going off-script today ✨
  • --prob_cutoff — probability cutoff for calling genotype (default 0)
  • --alternatives — print probabilities of all alternative genotypes. not just the winner, the whole friend group 🌈
  • --info — print information about individual
  • --no_genotypes — print only summary information, not actual genotypes. the tl;dr version, no cap
  • --model TYPE — model type. your options are full, diploid, or haploid. pick your fighter 🥊
  • --params PARAMS — model parameters. the whole lineup is error, p0, p1, p2, coverage, size, size2
  • --coverage NUM — average coverage of reads
  • -D — increase debug level. spam it if you're nosy, i support it 🫶

🌟 EXAMPLES 🌟

you could find some usage examples in:

/usr/share/doc/genometester/README.FastGT.md

fr fr go read it, it's giving documentation 💜

👑 SEE ALSO 👑

the whole squad, honestly 🫶

and that's the page, bestie!! this was the GenomeTester manual, version dated 31 May 2018, filed under GMER_CALLER(1). mwah, go call some genotypes 💖✨🎀

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