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

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