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Fig. 2 | BMC Genomics

Fig. 2

From: Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery

Fig. 2

Statistical comparison of variant discovery pipelines’ performance. A Box plots representing the F1 scores for different combinations of aligners and variant callers. B - E Pairwise comparison of tool performance for read aligners (B, C) and variant callers (D, E) using pass-filter SNP (B, D) and indel (C, E) calls. On (B-E) the color of the cell corresponds to the median difference in F1 scores between the first tool (on the OX axis) and the second tool (on the OY axis); n.s. - the difference is not significant, * - p < 0.05, ** - p < 0.01, *** - p < 0.001 in the Wilcoxon paired signed rank test. Read aligners: BW - BWA MEM, BT-E2E - Bowtie2 (end-to-end mode), IS - isaac4, NO - Novoalign; variant callers and filtering strategies: CL - Clair3, DV - DeepVariant, G1 - GATK HaplotypeCaller with 1D CNN filtering, G2 - GATK HaplotypeCaller with 2D CNN filtering, GH - GATK HaplotypeCaller with recommended hard filters. ST - Strelka2, FB - Freebayes, OS - Octopus with standard filtering, OF - Octopus with random forest filtering

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BMC Genomics

ISSN: 1471-2164

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