Table 1.
Overview of identified cancer variant interpretation tools, sorted by publication date. We indicate the type of interface (file or query based) for data input as well as the type of output, the accessibility of a online demo or the source code and the type of data integration and the corresponding update mechanisms. Details can be found in the supplementary data. PAS is available as an iOS app; therefore, online demo is marked in brackets.
| Tool | Cit. | Year | User interface | Output | Online demo | Source code | Data integration | Automatic KB update |
|---|---|---|---|---|---|---|---|---|
| ANNOVAR | [14] | 2010 | File based | Annotation | Materialized | Individual | ||
| SnpEff/ClinEff | [15] | 2012 | File based | Annotation | ✓ | Materialized | Bundled | |
| AnalyzeGenomes | [16] | 2014 | File based/query based | Result set | ✓ | Materialized | Individual | |
| GATK Funcotator | [17, 18] | 2015 | File based | Annotation | ✓ | Materialized | Bundled | |
| MyVariant.info | [19] | 2016 | Query based | Result set | ✓ | Materialized | Individual | |
| Ensemble Variant Effect Predictor (VEP) | [20] | 2016 | File based | Annotation | ✓ | ✓ | Materialized | Bundled |
| CanProVar | [21, 22] | 2017 | Query based | Result set | ✓ | Materialized | Unknown | |
| PathOS | [23] | 2017 | File based | Report | ✓ | ✓ | Materialized | Bundled |
| Houston Methodist Variant Viewer (HMVV) | [24] | 2017 | File based | Report | ✓ | Materialized | Bundled | |
| MTB-Report | [25] | 2018 | File based | Report | ✓ | Materialized | Unknown | |
| Smart Cancer Navigator | [26] | 2018 | Query based | Report | ✓ | ✓ | API based | API based |
| Clinical and Genomic Information System (CGIS) | [27] | 2018 | File based | Report | ✓ | Materialized | Unknown | |
| PanDrugs | [28] | 2018 | File based/ query based |
Report | ✓ | Materialized | Unknown | |
| PREDICT Variant Information System (VIS) | [29] | 2018 | Query based | Result set | ✓ | Materialized | Individual | |
| Sequence Variant Identification and Annotation Platform (SeqVItA) | [30] | 2018 | File based | Annotation | ✓ | Materialized | Bundled | |
| Precision Medicine Knowledgebase (PreMedKB) | [31] | 2019 | Query based | Report | ✓ | Materialized | Unknown | |
| Pathogenicity of Mutation Analyzer (PathoMAN) | [32] | 2019 | File based/ query based |
Result set | ✓ | Materialized | Unknown | |
| Variant Interpretation for Cancer (VIC) | [33] | 2019 | File based | Annotation | ✓ | Materialized | Bundled | |
| Translational Genomics expert (TGex) | [34] | 2019 | File based/ query based |
Report | ✓ | Materialized | Unknown | |
| PAS | [35] | 2020 | Query based | Result set | (✓) | Materialized | Individual | |
| AML Variant Analyzer (AMLVaran) | [36] | 2020 | File based | Report | ✓ | ✓ | Materialized | Bundled |
| Open Custom Ranked Analysis of Variants Toolkit (OpenCRAVAT) | [37] | 2020 | File based | Annotation | ✓ | Materialized | Individual | |
| VICC Meta-Knowledgebase (VICC MetaKB) | [38] | 2020 | Query based | Result set | ✓ | ✓ | Materialized | Individual |
| MIRACUM-Pipe | [39] | 2020 | File based | Report | ✓ | Materialized | Individual | |
| Molecular Tumor Board (MTB) Portal | [40] | 2020 | File based/ query based |
Report | ✓ | Materialized | Individual | |
| VarStack | [41] | 2020 | Query based | Result set | ✓ | Materialized | Unknown |