VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs

Abstract

Motivation: Genomic variations comprise a spectrum of alterations, ranging from single nucleotide polymorphisms (SNPs) to large-scale structural variants (SVs), which play crucial roles in bacterial evolution and species diversification. Accurately identifying SNPs and SVs is beneficial for subsequent evolutionary and epidemiological studies. This study presents VariantDetective (VD), a novel, user-friendly, and all-in-one pipeline combining SNP and SV calling to generate consensus genomic variants using multiple tools.

Results: The VD pipeline accepts various file types as input to initiate SNP and/or SV calling, and benchmarking results demonstrate VD's robustness and high accuracy across multiple tested datasets when compared to existing variant calling approaches.

Availability and implementation: The source code, test data, and relevant information for VD are freely accessible at https://github.com/OLF-Bioinformatics/VariantDetective under the MIT License.

Figure 1.

Performance and benchmarking of VD. (A, B) Benchmarking of VD against three SNP callers (A) and four SV callers (B) using 15 simulated datasets. SURVIVOR was used to simulate SNPs and different types of SVs in the assembly of representative L. acidophilus, E. coli, and B. mallei genomes. (C, D) Comparison of F1 scores of VD with 41 SNP calling pipelines (C). Overall accuracy of VD against two top SNP callers: DV and HC (D). F1 scores of 41 SNP calling pipelines, including DV and HC, were obtained from a previous study (Bush et al. 2020). (E, F) Performance of VD against four SV callers using benchmarking human SVs datasets, including recall (E) and the number of predicted SVs (F). Parameters used for each caller were taken from a previous benchmarking publication (Tham et al. 2020). The 2 or 3 callers represent the results obtained from a minimum consensus of two or three callers used to generate the final variant list. VD: VariantDetective; FB: Freebayes; HC: GATK HaplotypeCaller; CL: Clair3; NV: NanoVar; NS: NanoSV; CS: CuteSV; SI: SVIM; DV: DeepVariant.