Writing GATK walkers
I am looking into writing walkers for the GATK. I have been browsing the available documentation here in the forum. I have found some very useful examples but it seems to me that the documentation is not complete.
I have the feeling that I would get quickly stuck when I can't find further documentation on the different classes most used by the walkers. For instance if I want to understand the meaning of the stratifiedContexts parameter in the annotate method of the InfoFieldAnnotation class where can I find this?
My question is: Could you please point me to the best documentation outside of the examples in the forum and the code itslef? Is there an API documenation available?