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FIRECLOUD | Doc #10939 | TCGA Controlled Access Data

TCGA Controlled Access Data
Dictionary | Created 2017-12-14


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TCGA Controlled Access Data

Controlled Access data contains protected data that requires prior dbGaP authorization to access in FireCloud and the TCGA Data Portal. If you meet the Requirements to Access Controlled Access Data Workspaces in FireCloud, you can view and enter pre-populated TCGA Controlled Access Data workspaces.

Examples of TCGA Controlled Access Data

  • DNA Sequencing data, including Level 1 whole genome and whole exome, and Level 2 somatic and germline mutation calls (BAM and VCF files)

  • miRNA Sequencing data, including Level 1 miRNA sequence data for tumor samples (BAM files)

  • mRNA Sequencing data, including Level 1 mRNA sequence data for tumor samples (BAM and FASTQ files)

  • Total RNA Sequencing data, including Level 1 mRNA sequence data for tumor samples (BAM and FASTQ files)

  • DNA Methylation data, including Level 1 whole genome sequence after bisulfite treatment and Level 2 methylation and mutation calls (BAM and VCF files)

  • Exon Array-based Expression data, including Level 1 and Level 2 raw and normalized signals for tumor samples (CEL and .txt files)

  • Copy Number SNP data, including Level 1 raw data and for tumor samples and Level 2 unnormalized SNP, copy number, and LOH data (CEL, .idat, and.txt files)

  • Low-Pass DNA Sequencing data, include Level 1 whole genome sequence data and Level 2 DNA variants (BAM and VCF files)

  • Microsatellite Instability (MSI) data, including Level 1 fragment analysis results and summary files (FSA and .txt files)

  • De-identified phenotypes and genotypes for individual study subjects

  • Pre-computed univariate associations between genotype and phenotype

  • Pedigrees

You can view TCGA Data Levels & Data Types for a full list of Controlled Access data types.


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