| # Annotation Sources 🗄️ |
| Genome Nexus aggregates variant annotation from various sources. There are two types: |
|
|
| 1. Small sized annotations are stored as static data in the mongo database |
| directly. See the [genome-nexus-importer repo](https://github.com/genome-nexus/genome-nexus-importer) if you want to |
| update/change this data. |
| 2. 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: |
|
|
| https://docs.google.com/spreadsheets/d/1xML949NWzJGcvltjlquwSRIv79o13C_sfrVPAU5ci9Q/edit#gid=258442188 |
| |
| ## 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/ |
| |
