.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH PIQUE-INPUT "1" "July 2020" "pique-input 1.0" "User Commands"
.SH NAME
pique-input \- software pipeline for performing genome wide association studies
.SH SYNOPSIS
.B pique
\fI\,-i in_prefix -o out_prefix\/\fR
[\-d] [\-v] [\-f in_format] [\-k kinship]
[\-p pheno_file] [\-c covar_file [\-e n_pc]]
.SH OPTIONS
.SS Mandatory parameters:
.HP
\fB\-i\fR in_prefix: input prefix for the input files
.HP
\fB\-o\fR out_prefix: output prefix for the output files
.SS Optional parameters:
.HP
\fB\-d\fR debug: saves intermediate files for debugging
.HP
\fB\-v\fR verbose: display all output from plink and smartpca
.HP
\fB\-f\fR in_format: input file format (default = ped)
.IP
ped = requires in_prefix.ped & in_prefix.map files
tped = requires in_prefix.tped & in_prefix.tfam files
vcf = requires .vcf filename
.HP
\fB\-p\fR pheno_file: phenotype file name
.IP
Defaults to [in_prefix].pheno
.HP
\fB\-g\fR group[,group...]: genotype sub\-groups to be analysed
.HP
\fB\-n\fR number: minimum number of genotypes in sub\-group (default = 20)
.HP
\fB\-k\fR kinship: method to calculate kinship matrix
.IP
Either 'IBS' (default) or 'BN' methods
.HP
\fB\-c\fR covar_file: generate covariate file [out_prefix].covar
.IP
from SNP information in .ped file using smartpca (EIGENSOFT)
.HP
\fB\-e\fR n_pc: number of eigenvectors to keep from smartpca
.HP
\fB\-m\fR MAF: Minor Allele Frequency
.HP
\fB\-x\fR missing: maximum per\-SNP missing
.PP
Further details and examples are given in the 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.