Provided are systems and methods for improving efficiency in high throughput genotyping operations by implementing a unique workflow management architecture that permits faster and more accurate determination and evaluation of genotyping and haplotyping, and software to accomplish the same. The system provides a user with a highly-accurate summary and multiple-field breakdown of panels of genotyping data samples for batch approval and batch selection of ambiguous or potentially unique sample sets which can be selected for further analysis. Also provided are tools for evaluating and improving the operation of a genotyping laboratory to maximize the testing and typing of the significant quantities of raw data used in genotyping that are produced in high-throughput laboratory environments.