Table 5.
Software components of the pipeline.
| Software | Description of use in this pipeline | Version | Availability |
|---|---|---|---|
| vt | Decomposition and Normalization of Variants | v0.57721 | https://genome.sph.umich.edu/wiki/Vt |
| Variant Effect Predictor (VEP) | Variant Annotation | v84 | http://www.ensembl.org/info/docs/tools/vep/script/index.html |
| GEMINI | Storage of annotated variants | 0.30.1 | https://github.com/arq5x/gemini |
| OMIM API | Retrieval and linkage of OMIM terms to causative genes | As accessed on 28/06/19 | https://www.omim.org/api |
| Phenolyzer | Linkage of HPO terms to causative genes | v1.0.5 | http://phenolyzer.wglab.org |
| Phenoparser | Process and storage of OMIM and Phenolyzer results and generation of gene panels | v1.0.0 | https://github.com/TimoLassmann/Phenoparser |
| BCFtools | Manipulation of variant data files | v1.6 | http://www.htslib.org/download |
| HTSlib (includes tabix and bgzip) | Indexing variant data files | v1.6 | http://www.htslib.org/download |
| Grabix | Indexing variant data files | 0.1.8 | https://github.com/arq5x/grabix |
| R | Collation of data and generation of patient report files | 3.2.3 | https://www.r-project.org |