I am looking for a way to create an Illumina report, starting from IDAT files. I know how to do it with GenomeStudio in Windows, but I would need to produce the same file (with BAF and LRR columns) in the Linux environment. Do you know how I can do it? Thanks in advance for your reply!
I presume that you mean that you want to use GenomeStudio on linux? - have you seen this previous answer - A: Automate Illumina GenomeStudio With Python Script ?
Thanks for the suggestion, I read the answer given on the topic. My point is that I just need the BAF and LRR information and not the gtc. Does the AutoConvert do that? Unfortunately, I am not very good at coding.