I have raw data(idat files) from Illumina Omni5 genotyping platform. My main interest is to find the Copy Number Variation in these samples. Any open-source packages that work with this type of datasets would be helpful to know.
I have explored crlmm and DNAcopy from Bioconductor but just got errors processing the idat files from this platform.
Take a look at the illuminario R package: http://f1000research.com/articles/2-264/v1. It's used by crlmm, so maybe you'll have no better luck, though if you can read the intensity values from the chips then maybe you can roll your own solution to write something like PennCNV formatted input files.