For Developers
How can I download BAM index files (BAI files) using the API?
Submitted by Anonymous
on
BAI files are included with the download when using the GDC Data Transfer Tool to download BAM files.
When using the API to download BAM files, BAI files will only be included if the related_files=true parameter is specified together with the BAM UUID, for example:
https://api.gdc.cancer.gov/data/53f4ad60-0777-409c-a34d-ca4442dc9c44?related_files=true
Where can I find more information about the GDC data model?
Submitted by Anonymous
on
The GDC employs a hierarchical data model which requires metadata and files to be attached only at particular nodes or points in the hierarchy. If you have questions, please review the GDC Data Model or contact GDC Support.
How long do GDC authentication tokens remain valid?
Submitted by Anonymous
on
GDC authentication tokens remain valid for 30 days.
Where do I go to find code examples for using the GDC API?
Submitted by Anonymous
on
The GDC provides code examples in the GDC Application Programming Interface (API) User's Guide
Where do I go to report an issue or submit an inquiry about the GDC?
Submitted by Anonymous
on
The GDC provides helpdesk support for data submission and other issues. For information on the GDC helpdesk, please visit GDC Support.
How do I obtain an account to log in to the GDC?
Submitted by Anonymous
on
Generally, browsing indexed GDC metadata (such as information about the cases and files contained in the GDC Data Portal) does not require a login.
eRA Commons authentication and dbGaP authorization are required before accessing controlled data, which generally includes individually identifiable information such as low level genomic sequencing data and germline variants.
Controlled-access data users log in to the GDC using their eRA Commons accounts. The GDC then verifies that the user has authorization in dbGaP to access specific controlled datasets.
How do I query and download data from the GDC?
Submitted by Anonymous
on
The GDC provides several resources for querying and downloading data from the GDC including the GDC Data Portal for querying and downloading GDC data files, the GDC Data Transfer Tool for downloading large volumes of files, and the GDC Application Programming Interface (API) for performing programmatic queries and downloads.