The GDC processes data through several harmonization pipelines. If the process of harmonization reveals issues in the underlying data or if an error occurred during harmonization, the harmonized data files (e.g. BAMs or VCFs) will not appear in GDC data access tools.
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).
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.
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.
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.
System requirements for using the GDC Data Transfer Tool are available on the GDC Data Transfer Tool page. Additional details are in the GDC Data Transfer Tool User's Guide.
The GDC provides helpdesk support for data submission and other issues. For information on the GDC helpdesk, please visit GDC Support.
