PIQUE-RUN(1)

✨ PIQUE-RUN(1) ✨

User Commands 🎀 pique-run

💖 NAME 💖

pique-run — bestie, it's a whole software pipeline for doing genome wide association studies 🧬✨

🌸 SYNOPSIS 🌸

pique-run -i in_prefix [-n threads] [-o out_prefix] [-k kinship] [-c
cov_file] -t transform

🦋 OPTIONS 🦋

👑 Mandatory parameters:

• -i in_prefix — the input prefix for your .tped, .tfam and .pheno files. Yeah you literally cannot skip this one, it's the whole vibe. 🫶

🎀 Optional parameters:

• -n threads — how many threads you wanna throw at it. Defaults to 1 (so, like, solo mode 🐢).
• -o out_prefix — prefix for the output files. Defaults to [input_prefix], so if you don't say anything it just reuses whatever you gave -i. iconic behaviour honestly 💅
• -k kinship — which method gets used to calculate the kinship matrix. Either the 'IBS' method (that's the default, no cap) or the 'BN' method. Pick your fighter ⚔️
• -c cov_file — covariate file name. 🍓
• -t transform — phenotype transformation. Options are BC = Box-Cox, or the default = none (so no transformation at all, just vibes ✨).

More information about pique-run usage can be found in the PIQUE documentation 📚

💜 AUTHOR 💜

Tony Travis <tony.travis@abdn.ac.uk> and Alex Douglas <a.douglas@abdn.ac.uk 😭 (yes bestie, the bracket situation is exactly as the original has it, I'm not touching it)

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫡

okay so that's the whole thing — pique-run version 1.0, dated July 2020, and that's the tea 🍵💖 periodt 💅