Where can I find known variants, training and truth sets, and other resource files?
For general definitions of these terms, see this Dictionary entry.
If you're working with human data, you're in luck. We provide all resource files necessary for applying the Best Practices pipelines to human data as part of our Resource Bundle, and we provide specific recommendations on which sets to use for each tool in the variant calling pipelines, as well as default settings for all parameters. See the Best Practices documentation for details to that effect.
Unfortunately we're not currently able to provide centralized resources for non-human organisms. That means you will need to do some additional homework to find out what is available for your organism. In order to facilitate this process, we have created a forum section called Zoo & Garden specifically for the purpose of collecting information on this topic. We invite researchers who have experience in non-human genomics analysis to share their knowledge by contributing documentation to this section.