I want to recall SNPs from Illumina HumanOmni2.5-4v1. I have the raw data (`Grn.idat` and `Red.idat`) files, and also a matching `FinalReport.csv` which include the next columns:

    SNP Name    Sample Name    GC Score    Allele1- Forward    Allele2- Forward    Allele -Top    Allele2-Top    Allele1-Design    Allele2-Design    Allele1-AB    Allele2-AB    Theta    R    X    Y    X Raw    Y Raw    B Allele Freq,    Log R Ratio

And I have thousands of such files. How can I get the number of calls for a specific SNP?

Should I use the raw idat files, or CSVs? And if the answer is the CSVs, then which column, and how to interpret it?

Thanks
I finally ended up using R package named crlmm. It has a function named genotype.Illumina that does the recalling given the raw idat files.