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 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/
Last modified 1mo ago
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