What pipelines and repos help beginners with WGS variant calling and annotation?

[KyleC]

As a biology graduate student, my thesis is shifting towards computational biology, and I need to get up to speed on current genomics tools and databases for analyzing whole genome sequencing data. I have a foundational understanding of the concepts, but I'm struggling to choose between the myriad of available pipelines for variant calling and functional annotation. For researchers working in this space, what software stacks or public repositories have you found most reliable and well-documented for a beginner to start producing publishable quality analysis?