Comparison was made with controls of European descent from the Wellcome Trust Case Control Consortium using logistic regression algorithm from PLINK.  No single SNP passed the genomewide significant level of 5 × 10(-8) in the analysis of genotyped SNP in PLINK. 
PLINK
SNPs not genotyped by the array were imputed with 1000 Genomes Project data using the MaCH algorithm and minimac.  Postimputation analysis was done with the mach2dat algorithm using a logistic regression model. 
MaCH
SNPs not genotyped by the array were imputed with 1000 Genomes Project data using the MaCH algorithm and minimac. 
minimac
Postimputation analysis was done with the mach2dat algorithm using a logistic regression model. 
mach2dat