Statistical Analysis of Genotyping Data. There are a number of programs available to 
carry out GWAS.  One of the most useful is PLINK (PLINK: a tool set for whole-genome 
association and population-based linkage analyses (Purcell, Neale et al. 2007).  PLINK 
has been utilized in hundreds of GWAS analysis but more importantly it provides a set of 
useful tools to evaluate data quality and control for a number of inaccuracies that 
can lead to misclassification and, consequently decreased power, or alternatively increased 
false-positive rates. We propose several measures to improve overall data quality and
 many of these are implemented in PLINK.