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Fig. 2 | Genome Biology

Fig. 2

From: Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale

Fig. 2

Online performance comparison of Bystro, VEP, wANNOVAR, and GEMINI. Bystro, wANNOVAR, VEP, and GEMINI (running on Galaxy) we run under similar conditions. Total processing time was recorded for 1000 Genomes Phase 3 WGS VCF files, containing either the full dataset (2504 samples, 8.49 × 107 variant sites) or subsets (2504 samples and 5 × 104, 3 × 105, 1 × 106, and 6 × 106 variants). Only Bystro successfully processed more than 1 × 106 variants online; wANNOVAR (not shown) could not complete the smallest 5 × 104 variant subset; VEP could not complete more than 5 × 104 variants; and GEMINI/Galaxy could not complete more than 1 × 106 variants. Online, VEP outputted a restricted subset of annotation data compared to its offline version. GEMINI and Bystro (but not VEP) outputted whole-genome CADD scores, while only Bystro also returned whole-genome PhyloP and PhastCons conservation scores. Bystro was faster than GEMINI/Galaxy by 144–212× across all time points

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