Standardized Germline Variant Calling Performance Metrics
/GA4GH Benchmarking Team Releases Best Practices for Comparing Germline Variant Calls
NEW YORK (GenomeWeb) – Members of the benchmarking team of the Global Alliance for Genomics and Health have developed methods for producing standardized performance metrics for benchmarking small germline variant calls.
The GA4GH Benchmarking team brings together participants from research institutes, technology companies, government agencies, and clinical laboratories. It includes researchers from the National Institute of Standards and Technology (NIST), Illumina, Ontario Institute for Cancer Research, DNAnexus, and others.
As explained in a Nature Biotechnology paper published yesterday, the methods that they have developed address challenges associated with standardizing metrics like recall and precision, comparing different representations of variant calls, and stratifying performance by variant type and genome context. The team has made the code used for the benchmarking available in Github.
