I have recently performed a GWAS study, and I was very disappointed that some information from Illumina was concealed from me. In particular, I received from Illumina tech support a list of snps which they suggest to remove from the analyses. Since this list is not publicly available, I decided to share it here with you.
The following list contains SNP assays that we suggest removing from your Human610-quad/iM-duo results. Name
The following list contains SNP assays that we feel yield the correct result for the Human610-quad chips (or 1M-duo). The results from the other chips should not be used. Name