The mouse clicking interface of GenomeStudio is so unfriendly for large and continuous data production. - Do we have alternatives to this that can process Illumina genotyping array idat files? - Or do you have any suggestions to automate the GenomeStudio process with command lines? Thanks
The crlmm package in R should be able to do it. However, in my own experience it is difficult to run it for Omni5 generated data. I guess it depends on which genotype array you are using. Alternatively, beadarray should also be able to read idat files but I have not tried that package yet.
You can use Illumina proprietary GenCall algorithm to generate GTC files out of IDAT file, there are now two approaches:
(i) using the Illumina Array Analysis Platform
(ii) using the Illumina Beeline/AutoConvert software
I describe how to use either approach on Linux here