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

# pique-run(1)

software pipeline for performing genome wide association studies

## NAME

pique-run - software pipeline for performing 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: input prefix for .tped .tfam and .pheno files

### Optional parameters:

**-n** threads: number of threads. Defaults to 1

**-o** out\_prefix: prefix for output files. Defaults to \[input\_prefix\]

**-k** kinship: method used to calculate kinship matrix. Either 'IBS' (default) or 'BN' methods

**-c** cov\_file: covariate file name

**-t** transform: phenotype transformation (BC = Box-Cox, default = none)

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

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