Fig. 1. A simple vcfdist partial credit example.

A simple example of vcfeval and vcfdist evaluations, demonstrating vcfeval’s dependence on variant representation and the usefulness of partial credit. a Reference, query, and truth sequences, as well as the query and truth variant call files (VCFs). b vcfeval and c vcfdist count of true positive, false positive, false negative, and partial positive variants, as well as the calculated precision, recall, and F1 quality scores. Note that although both query VCF variant calls result in the exact same query sequence, the summary statistics differ. Partial credit alleviates this problem for vcfdist. d Distance-based summary statistics reported by vcfdist: edit distance, distinct edits, and alignment distance, which are independent of variant representation. An explanation of these summary statistics can be found in the Methods section.