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The GATK Methods for Bacterial Variant Discovery and Evaluation
To develop GATK methods for variant discovery and evaluation in bacteria, resolve inconsistent and diverse results from different research groups, and allow for the sharing of data and analysis globally to control bacterial transmission and antibiotic resistance.
Lack of computationally reproducible and interoperable software for bacterial variant analysis has forced researchers to use the human optimized GATK software due to its high sensitivity for low and variable allele fraction variants. However, the GATK has not been tested or optimized for non-human use cases. The GATK already has several tweaks to local assembly that improves sensitivity to low-allele fraction variants even in the case of highly-varying depths, which is a typical challenge in bacterial variant analysis. Detecting SNVs and indels at variable read depths is crucial for studying bacterial genetic heterogeneity, evolution, epidemiology, transmission, and antibiotic resistance mechanisms.