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Table 1 Average single-core runtimes of VCF files containing 50,000 variants passing individually through all filters with timings for each Annotation, Filtering, and Extended annotation modules

From: OVAS: an open-source variant analysis suite with inheritance modelling

Pipeline stage Module name Runtime (seconds)
  Adding genes 125
Annotation Adding function 28.7
  Adding Zygosity 0.81
Filtering Physical location filter 1.02
  Read depth filter 1.26
  Call quality filter 0.93
  AAF filter 143
  Mutation type filter 1.08
  Novel variant filter 1.12
  Same gene filter 22.5
  Same variant filter 26.1
  AD inheritance 0.83
Trait penetrance model AR inheritance 1.22
  XD inheritance 0.74
  XR inheritance 1.39
  Mosaicism 0.94
Extended annotation Isoform context 2.28
  Protein context 4.10
  Gene expression 145
  1. Trait Penetrance module timings are based on three VCFs consisting of a parent-offspring trio. Tests were run on a 2GHz dual-core processor with 4GB RAM