REPLY TO HUANG ET AL: Avoiding “one-size-fits-all” approaches to variant discovery

Huang et al argue that variant calling methods less conservative than GATK's Best Practices workflow increased false-positive variant discovery in our study of wild and cultivated potatoes, impacting diversity estimates. We disagree with their conclusion and highlight the rationale for the variant calling methods used in our study. Estimates of nucleotide diversity in crop species depend not only on variant calling methods but also genetic bottlenecks, ploidy, and reproductive mode. Thus, it is not surprising that outcrossing maize, watermelon, and potato report higher nucleotide diversity than inbreeding species with strong genetic bottlenecks such as tomato and soybean. However, variant counts generated for potato using GATK hard filtering were lower than those for both tomato and soybean, an unlikely outcome considering the biology of these species.