Submit Data

There has been long standing debate about prefixes for multiples of bytes. We have chosen to utilize the standard supported by the International System of Units (SI) where 1 gigabyte (GB) = 10⁹ bytes or 1 megabyte (MB) = 10⁶ bytes. This convention is also supported by the IEEE, EU, NIST, and the International System of Quantities. Where appropriate, we utilize the IEEE 1541 recommendations for binary representation where 1024³ bytes = 1 gibibyte (GiB) or 1024² bytes = 1 mebibyte (MiB).

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.

Recurrent data releases allow the GDC to version the data and allow users to reference the GDC version number in publications. GDC currently generates releases as needed, with a release every 2-3 months as a goal.

Uploaded and validated data is put in a workspace until the user formally submits the data to the GDC. This allows users to interact with the data before submitting. Once the data is submitted, the GDC will process applicable datasets (e.g. harmonize molecular data and generate high level data). After processing has been completed, the data is made publicly available according to GDC Data Sharing Policies.

Submitted BAM files are validated at the GDC for file integrity and format using md5sum checks, automated QC checks, and the Picard ValidateSamFiles tool. Sequencing quality is assessed using FASTQC, and additional quality metrics are gathered using tools like Picard and Samtools. Severe issues, such as high cross-sample contamination, may prevent the data from being released, but minor issues typically do not result in rejection. Instead, the GDC exposes many of the quality metrics so users may review them and do further filtering.

The study and Subject IDs must be registered in dbGaP. For additional details, please visit: Obtaining Access to Submit Data.

GDC authentication tokens remain valid for 30 days.

The GDC Data Transfer Tool uses sequential read/write for each file segment that is being transferred. By default, the tool executes multipart transfers, which results in multiple parallel, sequential read or write operations. To turn off multipart transfers, users can set the number of processes to 1.

The GDC Data Transfer Tool does not offer a setting to limit the bandwidth it uses.

The GDC Data Transfer Tool is recommended for transferring large datasets to or from GDC. For additional details, please visit the GDC Data Transfer Tool User’s Guide.