.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH PIQUE-RUN "1" "July 2020" "pique-run 1.0" "User Commands"
.SH NAME
pique-run \- software pipeline for performing genome wide association studies
.SH SYNOPSIS
.B pique-run
\fI\,-i in_prefix \/\fR[\fI\,-n threads\/\fR] [\fI\,-o out_prefix\/\fR] [\fI\,-k kinship\/\fR] [\fI\,-c cov_file\/\fR] \fI\,-t transform\/\fR
.SH OPTIONS
.SS Mandatory parameters:
.HP
\fB\-i\fR in_prefix: input prefix for .tped .tfam and .pheno files
.SS Optional parameters:
.HP
\fB\-n\fR threads: number of threads. Defaults to 1
.HP
\fB\-o\fR out_prefix: prefix for output files. Defaults to [input_prefix]
.HP
\fB\-k\fR kinship: method used to calculate kinship matrix. Either 'IBS' (default) or 'BN' methods
.HP
\fB\-c\fR cov_file: covariate file name
.HP
\fB\-t\fR transform: phenotype transformation (BC = Box\-Cox, default = none)
.PP
More information about pique\-run usage can be found in the PIQUE documentation
.SH AUTHOR
Tony Travis <tony.travis@abdn.ac.uk> and Alex Douglas <a.douglas@abdn.ac.uk
.PP
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.