Table 1.
Comparing different tools/properties, see Supplementary Material for details.
| Tool | Syntax | Annotation | I/O formats | Breakends | Speed |
|---|---|---|---|---|---|
| bcftools | Custom | VEP a | VCF, BCF | No | +++ |
| bio-vcf | Ruby/customb | - | VCF | No | - |
| filter_vep | Custom | VEP | VCF | No | --- |
| slivar | Js/customb | Customc | VCF, BCF | No | - |
| SnpSift | Custom | SnpEff | VCF | No | + |
| VcfFilterJdk | Java | VEP, SnpEffd | VCF, BCFe | No | ∘f |
| vembrane | Python | VEP, SnpEff | VCF, BCF | Yes | ++ |
a
Through +split-vep plugin.
b
Additionally ‘custom’ because some scenarios require complex Command Line Interface option combinations.
c
Special handling of impact annotations from bcftools, VEP or SnpEff.
d
EFF only.
e
VCF < v4.3, BCF < v2.1 only.
f
Manually estimated performance, since it is not included in the benchmark due to incompatible VCF version support and lack of conda packages.
Symbols used for speed classification range from --- (slowest) through ∘ (average) to +++ (fastest).