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Table 8 Comparison of runtime

From: The Ensembl Variant Effect Predictor

Tool Chr. 21 All
Annovar 0 m38.933 s (1732 v/s) 21 m50.037 s (3415 v/s)
SnpEff 1 m46.178 s (635 v/s) 46 m39.142 s (1598 v/s)
SnpEff (threaded)* 1 m21.046 s (832 v/s) 10 m28.274 s (7121 v/s)
VEP 0 m47.216 s (1428 v/s) 62 m9.107 s (1200 v/s)
  1. Two datasets from Illumina’s Platinum Genomes were used [93], both on the GRCh37 assembly: 67416 variants from chromosome 21 and the whole genome set of 4,474,140 variants. Each tool was configured to use the Ensembl release 75 gene set, with options configured for the fastest runtime. Run time and speed in variants per second (v/s) are shown. *SnpEff was run in threaded mode but multiple warnings and errors were produced during these runs.