Fig. 3.

Variant calling performance across five variant calling pipelines using the BWA-mem aligner. (A) SNS variant calling performance was evaluated when using the BWA-mem aligner with the following variant calling pipelines: Pilon, mpileup-call, Varscan2, GATK-HaplotypeCaller-HardFiltering, and GATK-HaplotypeCaller-CNN. (B) INDEL (1–15 bp) variant calling performance was evaluated when using the BWA-mem aligner with the five variant calling pipelines listed above. The mean precision and recall across all 36 isolates were calculated for each set of filtering parameters evaluated. All benchmarking results at the aggregate and individual sample level can be found in Supplementary File S24