Reply to Huang et al.: Avoiding “one-size-fits-all” approaches to variant discovery

Huang et al. (1) argue that variant calling methods less conservative than GATK’s Best Practices workflow (2) increased false-positive variant discovery in our study of wild and cultivated potatoes (3), impacting diversity estimates. We disagree with their conclusion and highlight the rationale for the variant calling methods used in our study. First, GATK Best Practices, developed at the Broad Institute, were specifically designed and optimized for human genomics and medical research. Variant calling methodology for human medical research utilizes parameters and validation thresholds not intended for universal application across genomic studies. GATK’s hard filter is openly presented as a bias-prone substitute to their preferred (human-specific) variant quality … [↵][1]1To whom correspondence should be addressed. Email: buell{at}msu.edu. [1]: #xref-corresp-1-1