Public Demo
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We have installed a public demo at the University of Cambridge to facilitate the testing and development for all users. We have loaded and indexed five different datasets organised in 3 projects and 5 studies, these cover the most typical data use cases today such as multi-sample VCF, family exomes, and genomes; or cancer somatic data. All documentation examples and tutorials use this demo installation.
OpenCGA public demo REST URL is available at . You can check REST API and documentation at .
We have created a read-only user called demouser with password demouser. As in most OpenCGA installations where normal users are not the owners of the data, demouser has been given VIEW access to all demo user data, this is a very common configuration in OpenCGA where the owner of the data grant access to other users. In this demo installation the owner of the data is demo user, while demouser user is the public user created to query data.
In this demo we have indexed 5 different genomic datasets. Data has been organised in three projects and five studies. These represents different assemblies and data types such as multi sample VCF, aggregated VCF or family genome or exome. The data is organised in 3 projects and 5 studies. You can find some useful information in this table:
Project ID - Name
Study ID - Name
VCF File Type
Samples
Variants
population
Population Studies GRCh38
1000g
1000 Genomes phase 3
WGS Multisample
2,504
82,587,763
uk10k
UK10K
WGS Aggregated
10,000
46,624,127
family
Family Studies GRCh37
corpasome
Corpas Family
WES Family Multisample
4
300,711
platinum
Illumina Platinum
GWS Family Multisample
17
12,263,246
In order to make this demo more useful to users we have loaded or simulated some clinical data, this allows to exploit OpenCGA analysis such as GWAS or clinical interpretation. You can find clinical data for each study in the following sections.
There is no possible clinical data in this study. This is a WGS aggregated dataset so no samples or genotypes were present in the dataset and, therefore, no Individuals or Samples have been created.
We simulated two different disorders and few phenotypes for the different members of the family. To be documented soon.
To be documented soon.
To be documented soon.
We loaded the 1000 Genomes pedigree file, you can find a copy at