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Appendix A: Available Fields
Appendix B: Key Terms
Appendix C: Format of Submission Queries and Responses
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Data Submission
Data Submission
Before Submitting Data to the GDC Portal
Data Submission Overview
Data Submission Portal
Data Upload Walkthrough
Submission Best Practices
Troubleshooting Guide
Release Notes
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Data Transfer Tool
Data Transfer Tool
Getting Started
Preparing for Data Download and Upload
Data Transfer Tool Command Line Documentation
Release Notes - Command Line
Data Transfer Tool UI Documentation
Release Notes - UI
Troubleshooting Guide
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Data Dictionary
Data Dictionary
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Data
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Introduction
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File Format: MAF
File Format: VCF
Bioinformatics Pipeline: DNA-Seq Analysis
Bioinformatics Pipeline: mRNA Analysis
Bioinformatics Pipeline: miRNA Analysis
Bioinformatics Pipeline: Copy Number Variation Analysis
Bioinformatics Pipeline: Methylation Analysis Pipeline
Bioinformatics Pipeline: Protein Expression
Aligned Reads Summary Metrics
Release Notes
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Encyclopedia
Encyclopedia
Index
ABSOLUTE LiftOver
Affymetrix SNP 6.0
Aggregated Somatic Mutation
Aligned Reads
Aliquot
Aliquot Ensemble Somatic Variant Merging and Masking
Analyte
Annotations
Annotations TCGA
Arriba
ASCAT2
ASCAT3
AscatNGS
BCGSC miRNA Profiling
Biospecimen Data
Birdseed
BRASS
Cancer Genomics Hub
Case
Center for Cancer Genomics
Clinical Data
Clinical Supplement
Controlled Access
Data Access Policy
Data Submitter
dbGaP
Entity
FM Simple Somatic Mutation
FoundationOne Annotation
FoundationOne Variant Aggregation and Masking
FPKM-UQ
FPKM
GATK4 MuTect2 Tumor-Only
GATK4 MuTect2 Tumor-Only Annotation
GDC API
GDC Data Portal
GDC Data Submission Portal
GDC Data Transfer Tool
GDC Documentation Site
GDC Web Site
Genomic Data Analysis Network
Genomic Data Commons
Harmonized Data
Latest Data
Manifest File
MD5 Checksum
MuSE
MuSE Annotation
Mutation Annotation Format
Mutation Annotation Format TCGAv2
MuTect2
MuTect2 Annotation
Pindel
Pindel Annotation
Redaction
Release Number
REST API
RNA-Seq
SeSAMe Methylation Beta Estimation
Seurat 10x Chromium
SNP Array-Based Data
STAR-Fusion
STAR 2-Pass Chimeric
STAR 2-Pass Genome
STAR 2-Pass Transcriptome
STAR Counts
TCGA Barcode
TCGA VCF 1.1v2
TCIA
UUID
Variant Call Format
Variant Type
VarScan2
VarScan2 Annotation
VCF LiftOver
Index
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