This repository hosts the work of the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team, which is developing standardized performance metrics and tools for benchmarking germline small variant calls. This Team includes representatives from sequencing technology developers, government agencies, academic bioinformatics researchers, clinical laboratories, and commercial technology and bioinformatics developers. We have worked towards solutions for several challenges faced when benchmarking variant calls, including (1) defining high-confidence variant calls and regions that can be used as a benchmark, (2) developing tools to compare variant calls robust to differing representations, (3) defining performance metrics like false positive and false negative with respect to different matching stringencies, and (4) developing methods to stratify performance by variant type and genome context. We also provide links to our reference benchmarking engines and their implementations, as well as to benchmarking datasets. See doc/standards/ for the current benchmarking standards and definitions.