Annotation Sources 🗄️
Genome Nexus aggregates variant annotation from various sources. There are two types:
- Small sized annotations are stored as static data in the mongo database directly. See the genome-nexus-importer repo if you want to update/change this data.
- For larger annotation services/databases we either run the full annotation service ourselves or the program pulls on the fly from other APIs and caches the result in the mongo database.
For a list of all supported variant annotation sources see this Google Sheet:
Versions
The static annotation sources are either stored directly in the mongo database or we run the annotation service ourselves. In both cases the version is guaranteed. For the dynamic annotion sources an external API is called and responses are cached on a per request basis. Given that the external API is outside of our control, no particular version is guaranteed, but we provide links to documentation of those APIs to find the currently live version.
Static annotation sources
| Algorithm | URL | Version |
|---|---|---|
| VEP | https://grch37.ensembl.org/info/docs/tools/vep/index.html | grch37 |
| Cancer Hotspots | https://www.cancerhotspots.org | From paper |
| 3D Hotspots | https://www.3dhotspots.org/#/home | From paper |
VEP includes various other annotations:
| Source | Version (GRCh38) | Version (GRCh37) |
|---|---|---|
| Ensembl database version | 103 | 103 |
| Genome assembly | GRCh38.p12 | GRCh37.p13 |
| GENCODE | 37 | 19 |
| RefSeq | 2020-09-29 (GCF_000001405.39_GRCh38.p13_genomic.gff) | 2019-11-01 (GCF_000001405.25_GRCh37.p13_genomic.gff) |
| Regulatory build | 1.0 | 1.0 |
| PolyPhen | 2.2.2 | 2.2.2 |
| SIFT | 5.2.2 | 5.2.2 |
| dbSNP | 154 | 153 |
| COSMIC | 92 | 90 |
| HGMD-PUBLIC | 2019.4 | 2019.4 |
| ClinVar | 2020-08/2020-09 | 2019-12 |
| 1000 Genomes | Phase 3 (remapped) | Phase 3 |
| NHLBI-ESP | V2-SSA137 (remapped) | V2-SSA137 |
| gnomAD | r2.1, exomes only (remapped) | r2.1, exomes only |
Dynamic annotation sources
These annotation sources are pulled on the fly. The version number is not guaranteed given that the data is cached in the mongo database.
| API | URL | Note |
|---|---|---|
| My Variant Info | https://myvariant.info | Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html |
| Mutation Assessor | http://mutationassessor.org/r3/ |