pique-input1
Software pipeline for performing genome wide association studies
Usage
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