OpenCGA uses a two-level structure to organise datasets, these are Projects and Studies and are used to organise HGVA data and metadata:
You can get more information about data organisation at OpenCGA Catalog Data Management. Projects and Studies have a unique alias to ease their usage from the command-line and REST API, you can find more information about how to query data programmatically at RESTful Web Services and Clients. Please, see next section the full list and organisation of the currently available Projects and Studies (datasets) in HVGVA.
In this sections you can find all datasets loaded in HGVA and how they are organised in Projects and Studies (see previous section).
Projects name (alias) | Studies | HGVA Version/Date | ||
---|---|---|---|---|
Name | Alias | v1 (Dec. 2016) | v2 (Jan. 2018) | |
Reference GRCh37 (reference_grch37) | 1000 Genomes Project GRCh37 | 1kG_phase3 | Phase 3 2016-05 | Phase 3 2016-05 |
Exome Sequencing Project (ESP6500) | ESP6500 | 2016-05 | 2016-05 | |
Exome Aggregation Consortium (ExAC) | EXAC | 0.3.1 2016-05 | 0.3.1 2016-05 | |
Genome of the Netherlands (GoNL) | GONL | Release 5 2016-05 | Release 5 2016-05 | |
UK10K Project | UK10k | 2016-05 | 2016-05 | |
DiscovEHR | DISCOVEHR | - | ||
Genome Aggregation Database (gnomAD Exomes) | GNOMAD_EXOMES | - | ||
Genome Aggregation Database (gnomAD Genomes) | GNOMAD_GENOMES | - | ||
Spanish Medical Genome Project (MGP) | MGP | 2016-12 | 2016-12 | |
Reference GRCh38 (reference_grch38) | 1000 Genomes Project GRCh38 | 1kG_phase3 | Phase 3 2016-10 | Phase 3 2016-10 |
ESP6500 | ESP6500 | - | ||
UK10K Project (*) | UK10K | - | ||
DiscovEHR (*) | DISCOVEHR | - | ||
Genome Aggregation Database (gnomAD Exomes) (*) | GNOMAD_EXOMES | - | ||
Genome Aggregation Database (gnomAD Genomes) (*) | GNOMAD_GENOMES | - | ||
Cancer GRCh37 (cancer_grch37) | QIMR Berghofer Melanoma | QIMR_Berghofer_Melanoma | 2016-12 | 2016-12 |
Chronic Myeloid Leukemia - Russian Academy of Medical Sciences | RAMS_CML | 2016-12 | 2016-12 | |
Platinum (platinum) | Illumina Platinum | illumina_platinum | 2015-08 | 2015-08 |
(*) Liftover carried out by Genomics England (GEL)
Variant annotation was carried out by the CellBase project. Please, check CellBase documentation for details on additional data sources: Data sources and species
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