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 <[email protected]> and Alex Douglas <[email protected]>
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.