PIQUE-INPUT(1)

✨ PIQUE-INPUT ✨

okay bestie, gather round, because pique-input is a whole software pipeline for performing genome wide association studies and it's about to become your new obsession 💅 no cap, this thing runs the whole GWAS glow-up for you and all you have to do is hand it a prefix. iconic behavior fr fr 🧬✨

🌈 SYNOPSIS 🌈

pique -i in_prefix -o out_prefix [-d] [-v] [-f in_format] [-k kinship]
      [-p pheno_file] [-c covar_file [-e n_pc]]

like… that's it. that's the whole vibe. two required flags and a lil pile of optional ones that are giving main character energy 🎀

👑 OPTIONS 👑

💖 Mandatory parameters:

these two? non-negotiable. the pipeline literally will not know what to do without them, bestie 😭

• -i in_prefix — the input prefix for the input files. your whole fam of input files hangs off this lil name 🫶
• -o out_prefix — the output prefix for the output files. everything pique spits out gets this name slapped on the front ✨

🦋 Optional parameters:

the fun section. mix and match, live your truth 💜

• -d — debug mode: saves intermediate files for debugging. lowkey a lifesaver when something's acting up and you need to see the receipts 👀
• -v — verbose: display all output from plink and smartpca. not me wanting to read every single line of output 🙈
• -f in_format — the input file format. defaults to ped, bestie. here are your options:
  • ped — requires in_prefix.ped & in_prefix.map files
  • tped — requires in_prefix.tped & in_prefix.tfam files
  • vcf — requires .vcf filename
• -p pheno_file — the phenotype file name. and if you don't say anything? it just defaults to [in_prefix].pheno, she's self-sufficient like that 💅
• -g group[,group...] — the genotype sub-groups to be analysed. yes you can list several, just comma them up 🍓
• -n number — minimum number of genotypes in sub-group. default = 20, so tiny groups get filtered out, sorry lil guy 😭
• -k kinship — the method to calculate the kinship matrix. either 'IBS' (which is the default, queen) or 'BN' methods 👑
• -c covar_file — generate covariate file [out_prefix].covar from SNP information in the .ped file using smartpca (EIGENSOFT). she's fancy 🌸
• -e n_pc — number of eigenvectors to keep from smartpca. this one's nested up in the -c situation, iykyk ✨
• -m MAF — Minor Allele Frequency. set it, love it, filter with it 🧚
• -x missing — maximum per-SNP missing. your tolerance threshold for missingness, periodt 💀

📖 Further details and examples are given in the documentation — go read it, bestie, it's giving required reading 💖

💜 AUTHOR 💜

Tony Travis <tony.travis@abdn.ac.uk> and Alex Douglas <a.douglas@abdn.ac.uk> — absolute legends, no notes 🫶

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. slay, thank you Andreas 🌈

and that's the whole page, bestie 💖 pique-input 1.0, born July 2020 — still serving looks, still running GWAS pipelines, still that girl 👑✨🎀