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