Data organisation

OpenCGA uses a hierarchical structure to organize datasets. Briefly, Projects, Studies and Cohorts are used to organize HGVA metadata:

Projects are entities which contain one or more Studies.
Study, in turn, represents a particular data set with/without samples metadata, cohorts, and obviously genomic variation data. For example, The 1000 Genomes Project is defined as a study in OpenCGA. Likewise, The Genome of the Netherlads or the Exome Aggregation Consortium are also two different studies, and so on.
Finally, a cohort is simply a set of samples defined within a study. For example, populations and super-populations within The 1000 Genomes Project are defined as cohorts. Thus, EUR, AMR or GBR are examples of cohorts.

Please, click on http://bioinfo.hpc.cam.ac.uk/hgva-1.0/... to get a full list of currently available datasets (studies) in HGVA and how they are organized in different projects.

Studies

Project	Studies	Version/Date
Project	Studies	HGVA v1 (Dec. 2016)	HGVA v2 (Jul. 2017)
Reference GRCh37	1000 genomes project GRCh37	Phase 3 2016-05
	1000 genomes project GRCh38	Phase 3 2016-10
	Exome Sequencing Project	2016-05
	Exome Aggregation Consortium	0.3.1 2016-05
	Genome of the Netherlands	Release 5 2016-05
	UK10K project	2016-05
	Spanish Medical Genome Project	2016-12
	QIMR Berghofer Melanoma	2016-12
	Chronic Myeloid Leukemia - Russian Academy of Medical Sciences	2016-12

Variant annotation was carried out by the CellBase project. Please, check CellBase documentation for details on additional data sources: Data sources and species