Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery.

The results show surprisingly large differences in the performance of cutting-edge tools even in high confidence regions of the coding genome. This highlights the importance of regular benchmarking of quickly evolving tools and pipelines. We also discuss the need for a more diverse set of gold standard genomes that would include samples of African, Hispanic, or mixed ancestry. Additionally, there is also a need for better variant caller assessment in the repetitive regions of the coding genome.