Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Why are some of the annotation values different with VariantAnnotator compared to UG or HC?
As featured in this forum question.
Two main things account for these kinds of differences, both linked to default behaviors of the tools:
The tools downsample to different depths of coverage
The tools apply different read filters
In both cases, you can end up looking at different sets or numbers of reads, which causes some of the annotation values to be different. It's usually not a cause for alarm. Remember that many of these annotations should be interpreted relatively, not absolutely.