The steps invloved in genome-wide association study of case-controls settings:

  1) QC.
  
     A) genotype quality check
     
     B) sex check
     
     C) QC FMISS - missing rate check

     D) relatedness and ancestry check

2) SNP imputation

      A) QC imputation

3) Association analysis (cases-control)

4) post-gwas analyeses