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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
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BMC Bioinformatics

ISSN: 1471-2105

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