Program

Select a program among those available at the Genomic Data Commons portal.

TARGET - Therapeutically Applicable Research To Generate Effective Treatments TCGA - The Cancer Genome Atlas

Disease

Select a disease among those available for the previously selected program.

Data Type

Select a data type among experiments, clinical, and biospecimen data.
Please refer to the following link for a detailed documentation about the reference genome used by GDC:
https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files

Content Customization

Select what kind of information will be printed on the generated data.
This section is activated if you only want to convert the current data set.
The following fields are additional.
The chromosome, start position, end position, and strand information will always be present.

Please refer to the following link for a detailed documentation about what kind of information are reported in the original GDC data:
https://gdc.cancer.gov/about-data/data-harmonization-and-generation/genomic-data-harmonization-0

It is worth noting that the following section is scrollable.

Select All

Empty

Clinical and Biospecimen Filter

Filter the GDC experiments using their associated clinical and biospecimen information.
Leave these fields empty to select all available data.

Please refer to the following links for a detailed documentation about clinical and biospecimen attributes:
https://gdc.cancer.gov/clinical-data-elements
https://gdc.cancer.gov/about-data/data-harmonization-and-generation/clinical-data-harmonization
https://gdc.cancer.gov/about-data/data-harmonization-and-generation/biospecimen-data-harmonization

Note: for the TARGET program this section is not available due to the unconventional format of the original Clinical and Biospecimen Supplements.

Attribute

Value

Add Filter

Output Selection

Select the first checkbox if you want to preserve the original GDC data, and the second checkbox to automatically convert them in BED, GTF, CSV, or JSON format or in TXT format in the case of Clinical and Biospecimen Supplements.

Note: the Clinical and Biospecimen Supplements related to the TARGET program cannot be converted

Preserve original GDC data

Convert GDC data to format