PIQUE-INPUT(1) | User Commands | PIQUE-INPUT(1) |
pique-input - software pipeline for performing genome wide association studies
pique -i in_prefix -o out_prefix [-d] [-v] [-f in_format] [-k kinship] [-p pheno_file] [-c covar_file [-e n_pc]]
-i in_prefix: input prefix for the input files
-o out_prefix: output prefix for the output files
-d debug: saves intermediate files for debugging
-v verbose: display all output from plink and smartpca
-f in_format: input file format (default = ped)
-p pheno_file: phenotype file name
-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
-c covar_file: generate covariate file [out_prefix].covar
-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
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.
July 2020 | pique-input 1.0 |