---
name: "pique-input"
section: "1"
platform: "linux"
package: "pique"
version: "1.1-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pique-input"
---

# pique-input(1)

software pipeline for performing genome wide association studies

## NAME

pique-input - software pipeline for performing genome wide association studies

## SYNOPSIS

**pique** *-i in\_prefix -o out\_prefix* \[-d\] \[-v\] \[-f in\_format\] \[-k kinship\] \[-p pheno\_file\] \[-c covar\_file \[-e n\_pc\]\]

## OPTIONS

### Mandatory parameters:

**-i** in\_prefix: input prefix for the input files

**-o** out\_prefix: output prefix for the output files

### Optional parameters:

**-d** debug: saves intermediate files for debugging

**-v** verbose: display all output from plink and smartpca

**-f** in\_format: input file format (default = ped)

-

  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: phenotype file name

-

  Defaults to \[in\_prefix\].pheno

**-g** group\[,group...\]: genotype sub-groups to be analysed

**-n** number: minimum number of genotypes in sub-group (default = 20)

**-k** kinship: method to calculate kinship matrix

-

  Either 'IBS' (default) or 'BN' methods

**-c** covar\_file: generate covariate file \[out\_prefix\].covar

-

  from SNP information in .ped file using smartpca (EIGENSOFT)

**-e** n\_pc: number of eigenvectors to keep from smartpca

**-m** MAF: Minor Allele Frequency

**-x** missing: maximum per-SNP missing

Further details and examples are given in the documentation

## AUTHOR

Tony Travis \<tony.travis@abdn.ac.uk\> and Alex Douglas \<a.douglas@abdn.ac.uk\>

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