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Fig. 4 | Genome Medicine

Fig. 4

From: A variant by any name: quantifying annotation discordance across tools and clinical databases

Fig. 4

Summary of Ground Truth set HGVS syntax assessment. a Fraction of unique transcript accessions and versions in the Ground Truth set that were available to the tools SnpEff (snpeff), VEP (vep), and Variation Reporter (vr). If a transcript was not accessible to the tool, the variant could not be annotated with respect to that transcript. b Exact concordance of HGVS syntax at the coding (left) and protein (right) levels among the tools. c Accuracy of annotation across variants (total nā€‰=ā€‰121) described as exact (turquoise) and equivalent (light turquoise). Fraction shown is with respect to annotations on the relevant transcripts on the test set. d Accuracy of annotation by variant type across the tools. Variant types evaluated were: deletions (del), insertions and deletions (indel), duplications (dup), insertions (ins), and single nucleotide variants (SNVs)

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