Hey everyone. I am currently working on automating a SNP pipeline and need some help figuring out how to interface Python with GenomeStudio. I want to be able to pass input from a python script into GenomeStudio so that the entire analysis process can be automated and manual intervention is only required rarely. Does anyone have any experience with this? I've done a few Google searches and haven't come up with anything.

Thanks,
Travis Couture
Not exactly automating GenomeStudio, but what you could do is turn on AutoConvert on the iScan instrument and have it generate gtc files for each sample in your experiment. Then you can use the recently published open-source Python gtc file parser from Illumina to write a script for generating reports or whatever else you want to do with the data: https://github.com/Illumina/BeadArrayFiles. In the examples folder of that repo, there's an example script that lets you generate final report files from gtc files, thereby letting you avoid having to use GenomeStudio at all.

Or if you're working with idat files instead, what you could do is install and run AutoConvert off the instrument and write some Python code to go from idat + bpm + egt --AutoConvert--> gtc --python gtc file parser--> reports