GDC FAQs

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.

GDC data is stored in a secure FISMA-compliant facility. Access to controlled data requires authorization via dbGaP. See Data Access Processes and Tools for more information.

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.

See Obtaining Access to GDC Data and Resources for more information on data download, and Obtaining Access to Submit Data for information on data submission.

The GDC provides helpdesk support for data submission and other issues. For information on the GDC helpdesk, please visit GDC Support.

Users can perform advanced SQL-like queries using the GDC Data Portal Search interface. Instructions on using the GDC Data Portal Search interface are available in the GDC Data Portal 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 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.

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

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.

GDC authentication tokens remain valid for 30 days.

The GDC validates genomic data (BAM files) using FASTQC and Picard. For additional details, please visit: GDC Data Harmonization.

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.

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 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.

HIPAA guidelines require that patients with ages greater than 89 years be aggregated into a single age category. This is to limit the ability to positively identify these individuals. In practice this will impact the values reported in several fields. We have chosen to accurately display the age at diagnosis, but fields that give dates or time periods after this benchmark may be compressed. This may include such fields as "Days to last follow up", "Days to last known disease status", "Days to recurrence", "Days to death", and "Year of death". Other fields found in clinical supplement files may also be impacted. In the Data Portal you will only see ages of less than or equal to 90. Individuals over 89 will all appear as 90 years old.

The following web browsers are supported for use with the GDC Data Portal, Submission Portal, Website, and Documentation site.

• Most recent supported stable version of Microsoft Edge
• Most recent stable version of Google Chrome
• Most recent stable version of Mozilla Firefox

The GDC provides access to both open and controlled datasets. To access controlled datasets, users must obtain appropriate authorization through dbGaP. See Obtaining Access to Controlled Data for instructions on applying for access through dbGaP.

The GDC Data Portal is a web-based application that is limited by browser and network constraints. If a system timeout occurs when downloading files, please use the GDC Data Transfer Tool or contact the GDC Help Desk.

Capture kit information is provided by the GDC API at the read group level, where available. In some cases, additional information may be available in SRA XML files.

The relevant read_group properties returned by the GDC API are:

1. target_capture_kit_name
2. target_capture_kit_catalog_number
3. target_capture_kit_vendor
4. target_capture_kit_target_region

The target_capture_kit_target_region field provides a URL for the capture kit target file, distributed by the kit manufacturer or by the research program. Bait/probe files can sometimes be found at the same URL; or a URL to the bait/probe file may be available in the SRA XML file.

Note: Some BAM files include information from multiple read groups, and sometimes read groups produced with different capture kits are included in the same BAM file. Tools are available for splitting BAM files into read groups, e.g. bamutil.

Note: Target and bait/probe files may use an older reference genome, so liftover may be required for certain applications.

Harmonized BAM files from RNA-seq and DNA-seq experiments will contain both mapped and unmapped reads, if available. Unmapped reads are not distributed separately.

Raw sequencing files submitted to the GDC are processed using GDC Genomic Data Alignment pipelines. The processed data are made available in the GDC Data Portal as BAM files containing aligned reads and unmapped reads (if available). No reads are hard-clipped, but reads that were flagged as "failed" during an Illumina sequencing run are discarded.

Third-party tools such as biobambam2 or Samtools fastq can convert these files to FASTQ sequencing data. Note that DNA-Seq quality scores are modified during the score recalibration co-cleaning step, so third-party tool parameters must be set to retrieve the original scores (biobambam2: tryoq=1; samtools fastq: -O). Because GDC harmonized BAM files may contain multiple read groups, the conversion parameter should be set to retain read group IDs in the generated FASTQ files (biobambam2: outputperreadgroup=1; samtools: samtools split).

The file detail page and the metadata files accessible from that page (if available) can be used to determine the difference between files that share the same filename. For example, the files may be associated with different aliquots, or different patients.

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 

Alternatively, users can determine the BAI file UUID from the API files endpoint by supplying the BAM UUID. The BAI file UUID can then be used to download the BAI file from the data endpoint.

https://api.gdc.cancer.gov/files/53f4ad60-0777-409c-a34d-ca4442dc9c44?pretty=true&expand=index_files 

https://api.gdc.cancer.gov/data/60cefd89-b428-46b7-b5b0-3b6e2743ab20

Note: BAI files are not available for sliced BAM files.

The availability of follow-up data is specific to the project and associated study.

For the Multiple Myeloma Research Foundation (MMRF) Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile (CoMMpass) study, longitudinal information was generated to track patients over the course of their disease. This data is available in the GDC by viewing the clinical follow-up data available for download on each case page in the GDC Data Portal or by querying the GDC API.

For TCGA, follow-up data is available for specific TCGA studies and made available for download in associated clinical supplement files (i.e. clinical XML, biotabs). Follow-up data can be different for the different TCGA studies.

Submitting treatment data is optional as not all projects are associated with treatment studies. For TCGA projects, for example, not all projects and cases have treatment data. For TCGA projects with treatment data, information is available in applicable clinical supplement files (i.e. clinical XML, biotabs). For other project associated with treatment studies in which the treatment data has been submitted to the GDC, treatment data is available for download in JSON and TSV format. These studies may also contain clinical supplement files.

The TCGA marker and other landmark cancer genomics papers, as well as associated supplemental files, are available on the GDC Publication Pages. The Publication Pages provide access to publication information and supplementary files.

The GDC harmonizes data across projects. This includes aligning the genomic data to a common reference genome (HG38) and generating higher level data using GDC bioinformatics pipelines. Other repositories may process the data differently.

For example, TCGA data in cBioPortal uses the original mutation data generated by the individual TCGA sequencing centers. The source of the data is the Broad Firehose (or the publication pages for data that matches a specific manuscript). These data are usually a combination of two mutation callers, but they differ by center (typically a variant caller like MuTect plus an indel caller), and sequencing centers have modified their mutation calling pipelines over time. TCGA data in the GDC is harmonized with the latest reference genome (GRCh38). Mutations are called using four variant callers: MuTect, VarScan2, MuSE, and Pindel.

TCGA “collection” represents the collection of the sample for TCGA, whereas “procurement” represents the removal of tissue from the patient.

The GDC supports the submission of clinical and biospecimen supplements. Supplemental files can be downloaded from the GDC by searching for the Data Type "Clinical Supplement" or "Biospecimen Supplement" from the facet search in the GDC Data Portal Repository. For TCGA data, the supplement data is provided in XML documents and tab delimited files (biotabs). These files, in varying degrees, provide information on marker status (e.g. EBV status), treatment regimen, slide magnification, histology distinctions, and staging questions.

RNA-Seq
• Replaced all RNA-Seq data including: Alignments, Gene Expression (STAR) + New Normalization, Transcript Fusion
• Removed HTSeq Files
• Re-harmonized TCGA data to use the newer pipeline

WXS/Targeted Sequencing
• Generated and versioned new annotated somatic mutations and Ensemble MAFs
• Re-harmonized TCGA data to use the newer pipeline (alignments + mutation calls)

WGS
• Generated and versioned structural variant and gene level copy number data

Methylation
• Re-harmonized TCGA methylation data to use the new SeSAMe pipeline

scRNA-Seq
• Generated and versioned CPTAC-3 scRNA-Seq data

Other
• Replaced gene level copy number files for TCGA with those harmonized using ASCAT
• Replaced somatic mutation files for FM-AD and transitioned to aliquot-level MAFs
• Replaced all GENIE files

The primary reasons for the fewer open-access mutations are from two strategies that improve quality: 1) TCGA is now using a 2-caller ensemble, instead of a single caller; 2) Removal of variants outside of the target capture region, instead of a combined “target capture + GAF exonic region”. Additionally, TCGA was the original project in which GDC open-access variants were produced and used variant rescue steps that only applied to TCGA. To keep the TCGA variant-calling pipeline consistent across projects, GDC is no longer rescuing MC3 and TCGA validation variants.

Although GENCODE v22 data cannot be browsed in the GDC Data Portal, it can still be downloaded using the GDC Data Transfer Tool or API. You will need to either have a previous manifest or use known UUIDs to download v22 files.

For the reference genome, the GDC has been using an augmented version of GRCh38.p2 (with additional decoy sequences and virus sequences) since inception. The GDC does not use alternative contigs, and only derives high-level data from the major chromosomes, so the same reference genome is used for both gene model GENCODE v22 (from Data Release 1 to 31) and GENCODE v36 (from Data Release 32). As future versions of the reference genome are released, e.g., GRCh39, the GDC will evaluate the benefits of updating data to utilize the new version. By updating the reference genome, the GDC would expect to re-process all data sets. For information on the reference genome used by the GDC, please refer to the GDC Reference Files.

For workflow updates, the GDC prefers to keep the workflow stable, and will not update unless there are necessary updates such as updates of the reference genome or gene model, or major algorithm updates in the tools that could result significant changes in the generated data. When workflow updates are actually needed, the GDC categorizes them as either major updates or minor updates depending on whether the update significantly affects the output data. The GDC will re-process all existing data sets in major workflow updates, and such examples include transitioning the RNA-Seq genomic BAM alignment workflow into a new version that generates three BAMs and STAR counts; and updating the MAF workflow to add additional functions to the MAF files. Minor updates mostly happen to resolve bugs, security issues, and/or compatibility issues. For example, the GDC DNA-Seq alignment workflow has been updated several times to address quality issues from various submitted data; however, because the main alignment algorithm remains almost the same, the GDC does not need to re-process all the data sets for these minor updates.

Any germline SNP calls are not available for exploration in the GDC Data Portal. Instead, alignments for germline data are available under controlled access. Users with appropriate access may use the alignments to generate germline variants.

Some somatic variants callers, such as MuTect2, also output somatic calls with some level of germline possibilities, such as those labelled as "germline_risk". Please note that these calls are, by no means, germline variants. They are somatic calls with boundary probability of germline risks.

The SomaticSniper whole exome variant caller was one of the first generation somatic mutation callers developed by the scientific community. It works the best with blood cancer that has high level of tumor-in-normal contaminations, but is often overly permissive for solid tumors. Since our first data release in 2016, the GDC has gradually adopted newer tools or new tool versions, and has transited the focus of somatic variant calling from any single caller to multi-caller ensemble.

After comparing ensemble calls with and without SomaticSniper and also receiving feedback from the authors of SomaticSniper, the GDC decided to remove this tool from our production in Data Release 35. The GDC still maintains other four whole exome variant callers, including MuSE, MuTect2, Pindel, and VarScan2.

Generally any WGS data should have associated structural variant files (BEDPE) except in the cases in which either there are no tumor/normal matches or when variant calling has not been implemented yet.

Filtering in Cohort Builder results in a set of cases. Cases typically have available data for multiple Experimental Strategies (e.g., cases with RNA-Seq data can also have DNA-Seq data). As such, when navigating to Repository additional data besides RNA-Seq data is displayed. Repository filters are file based. When filtering Repository by Experimental Strategy (e.g., RNA-Seq) only files associated with the Experimental Strategy are displayed.

To view the top frequently mutated genes for a cohort, first build a cohort using the Cohort Builder and then select the Mutation Frequency tool in the Analysis Center

Filtering in Cohort Builder results in a set of cases. A case can have multiple diagnosis and tissues or organ of origins may be related to a secondary diagnosis.