I've been trying to find a resource for understanding the various steps in the GATK pipeline or more generally, mapping and alignment, and variant calling in general. There seems to be a huge learning curve involved and every resource I've come across assumes you've worked with the data for quite a while or you're super smart and able to figure out what's unsaid.
Even a concept as simple as how the forward and reverse reads are generated, and what strand bias is exactly, is buried under mountains of technical documents.
I've checked out the broadE videos, and they are quite useful. But is anyone aware of any other good introductory resources that give a broad overview of "how we do genomics", and possibly highlighting the difficulties we might encounter with determining what "truth" is, and the hurdles we may encounter? A book or real-life examples would be nice.