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.
Could anyone help me with two questions in comparing my vcf file to gold standard?
1. Regarding sites present in my vcf but absent in gold standard, are they ignored?
2. Regarding sites absent in my vcf but present in gold standard, are they assumed 0/0?