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.