PLINK is a free computational package that can be used for genome association analyses.
Data for PLINK should be in PED and MAP files.
PED files are space or tab delimited files, and need to start with the
following 6 columns: Family ID, Individual ID, Maternal ID, Paternal ID, Sex,
and Phenotype.
Sex should be coded with 1=male; 2=female; and any other value meaning unknown.
MAP files describe markers, and should contain only four columns: chromosome
(1-22, X, Y, or 0 if unplaced), rs\# or SNP ID, Genetic distance
(in the morgan unit), and Base-pair position (bp units).
There is more information about these file types on the PLINK website.