Genomic Data Commons Data Transfer Tool on Quest

Downloading data from the Genomic Data Commons onto Quest via gdc-client

Genomic Data Commons

The National Cancer Institute's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine.

To download genomics data from the Genomic Data Commons onto Quest, PIs must have an electronic Research Administration (eRA) commons account from the National Institutes of Health that has been given DBGap access for the Genomic Data Commons. Once this access has been granted by the NIH, PIs can then disseminate Genomic Data Commons access to other individuals in their lab. De-identified data can then be downloaded from the Genomics Data Portal onto Quest into the PI's allocation for computational research purposes, using gdc-client.

Using gdc-client

At the command line on Quest in the directory that you'd like to transfer the Genomic Data Commons data into, type:

module load gdc-client

Help is available by typing:

gdc-client --help

Additional instructions for using gdc-client can be found on the National Cancer Institute's webinar on using the GDC Data Transfer Tool.

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Article ID: 1700
Thu 5/12/22 12:39 PM
Tue 1/10/23 12:52 PM