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mkdocs.yml
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---
copyright: '© 2015-2024'
extra:
dictionary_app_root: /apps/dictionary
dictionary_viewer_page_id: Viewer
encyclopedia_entries_page_title: EncyclopediaEntries
encyclopedia_page_title: Encyclopedia
gdcmvs_app_root: /apps/gdcmvs
gdcmvs_viewer_page_id: Search
nav_exclude:
- EncyclopediaEntries
project_description: GDC Docs
project_org: GDC
project_root_dir: /
version: 1.0
analytics:
provider: custom
extra_css:
- stylesheets/gdc-common.css
- stylesheets/homepage.css
- stylesheets/font-awesome-4.5.css
markdown_extensions:
- tables
- pymdownx.superfences
- pymdownx.tabbed:
combine_header_slug: true
alternate_style: true
slugify: !!python/object/apply:pymdownx.slugs.slugify
kwds:
case: lower
- pymdownx.details
nav:
- Home: index.md
- API:
- Getting Started: API/Users_Guide/Getting_Started.md
- Search and Retrieval: API/Users_Guide/Search_and_Retrieval.md
- Downloading Files: API/Users_Guide/Downloading_Files.md
- Data Analysis: API/Users_Guide/Data_Analysis.md
- BAM Slicing: API/Users_Guide/BAM_Slicing.md
- Submission: API/Users_Guide/Submission.md
- Python Examples: API/Users_Guide/Python_Examples.md
- GraphQL Examples: API/Users_Guide/GraphQL_Examples.md
- System Information: API/Users_Guide/System_Information.md
- Additional Examples: API/Users_Guide/Additional_Examples.md
- 'Appendix A: Available Fields': API/Users_Guide/Appendix_A_Available_Fields.md
- 'Appendix B: Key Terms': API/Users_Guide/Appendix_B_Key_Terms.md
- 'Appendix C: Format of Submission Queries and Responses': API/Users_Guide/Appendix_C_Format_of_Submission_Requests_and_Responses.md
- Release Notes: API/Release_Notes/API_Release_Notes.md
- Download PDF: /API/PDF/API_UG.pdf
- Data Portal:
- Getting Started: Data_Portal/Users_Guide/getting_started.md
- Quick Start: Data_Portal/Users_Guide/quick_start.md
- Tutorial Videos: Data_Portal/Users_Guide/Video_Tutorials.md
- Cohort Builder: Data_Portal/Users_Guide/cohort_builder.md
- Analysis Center: Data_Portal/Users_Guide/analysis_center.md
- Repository: Data_Portal/Users_Guide/Repository.md
- Projects: Data_Portal/Users_Guide/Projects.md
- BAM Slicing: Data_Portal/Users_Guide/BAMslicing.md
- Clinical Data Analysis: Data_Portal/Users_Guide/clinical_data_analysis.md
- Cohort Comparison: Data_Portal/Users_Guide/cohort_comparison.md
- Cohort Level MAF: Data_Portal/Users_Guide/cohortMAF.md
- Gene Expression Clustering: Data_Portal/Users_Guide/gene_expression_clustering.md
- Mutation Frequency: Data_Portal/Users_Guide/mutation_frequency.md
- OncoMatrix: Data_Portal/Users_Guide/oncomatrix.md
- ProteinPaint: Data_Portal/Users_Guide/proteinpaint_lollipop.md
- Sequence Reads: Data_Portal/Users_Guide/proteinpaint_bam.md
- Set Operations: Data_Portal/Users_Guide/set_operations.md
- For Developers: Data_Portal/Users_Guide/Developers_Guide.md
- Release Notes: Data_Portal/Release_Notes/Data_Portal_Release_Notes.md
- Download PDF: Data_Portal/PDF/Data_Portal_UG.pdf
- Data Submission:
- Before Submitting Data to the GDC Portal: Data_Submission_Portal/Users_Guide/Checklist.md
- Data Submission Overview: Data_Submission_Portal/Users_Guide/Data_Submission_Overview.md
- Data Submission Portal: Data_Submission_Portal/Users_Guide/Data_Submission_Process.md
- Data Upload Walkthrough: Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md
- Submission Best Practices: Data_Submission_Portal/Users_Guide/Best_Practices.md
- Troubleshooting Guide: Data_Submission_Portal/Users_Guide/Troubleshooting.md
- Release Notes: Data_Submission_Portal/Release_Notes/Data_Submission_Portal_Release_Notes.md
- Download PDF: Data_Submission_Portal/PDF/Data_Submission_Portal_UG.pdf
- Data Transfer Tool:
- Getting Started: Data_Transfer_Tool/Users_Guide/Getting_Started.md
- Preparing for Data Download and Upload: Data_Transfer_Tool/Users_Guide/Preparing_for_Data_Download_and_Upload.md
- Data Transfer Tool Command Line Documentation: Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md
- Release Notes - Command Line: Data_Transfer_Tool/Release_Notes/DTT_Release_Notes.md
- Data Transfer Tool UI Documentation: Data_Transfer_Tool/Users_Guide/Data_Download_DTT_UI.md
- Release Notes - UI: Data_Transfer_Tool/Release_Notes/DTT_UI_Release_Notes.md
- Troubleshooting Guide: Data_Transfer_Tool/Users_Guide/Appendix_B_TroubleShooting.md
- Download PDF: Data_Transfer_Tool/PDF/Data_Transfer_Tool_UG.pdf
- Data Dictionary:
- About: Data_Dictionary/index.md
- Viewer: Data_Dictionary/viewer.md
- Search: Data_Dictionary/gdcmvs.md
- Release Notes: Data_Dictionary/Release_Notes/Data_Dictionary_Release_Notes.md
- Data:
- Introduction: Data/Introduction.md
- GDC Data Model: Data/Data_Model/GDC_Data_Model.md
- Data Security: Data/Data_Security/Data_Security.md
- 'File Format: MAF': Data/File_Formats/MAF_Format.md
- 'File Format: VCF': Data/File_Formats/VCF_Format.md
- 'Bioinformatics Pipeline: DNA-Seq Analysis': Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline.md
- 'Bioinformatics Pipeline: mRNA Analysis': Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline.md
- 'Bioinformatics Pipeline: miRNA Analysis': Data/Bioinformatics_Pipelines/miRNA_Pipeline.md
- 'Bioinformatics Pipeline: Copy Number Variation Analysis': Data/Bioinformatics_Pipelines/CNV_Pipeline.md
- 'Bioinformatics Pipeline: Methylation Analysis Pipeline': Data/Bioinformatics_Pipelines/Methylation_Pipeline.md
- 'Bioinformatics Pipeline: Protein Expression': Data/Bioinformatics_Pipelines/RPPA_intro.md
- Aligned Reads Summary Metrics: Data/Bioinformatics_Pipelines/Aligned_reads_summary_metrics.md
- Release Notes: Data/Release_Notes/Data_Release_Notes.md
- Download PDF: Data/PDF/Data_UG.pdf
- Encyclopedia:
- Index: Encyclopedia/index.md
- ABSOLUTE LiftOver: Encyclopedia/pages/ABSOLUTE_LiftOver.md
- Affymetrix SNP 6.0: Encyclopedia/pages/Affymetrix_SNP_6.0.md
- Aggregated Somatic Mutation: Encyclopedia/pages/Aggregated_Somatic_Mutation.md
- Aligned Reads: Encyclopedia/pages/Aligned_Reads.md
- Aliquot: Encyclopedia/pages/Aliquot.md
- Aliquot Ensemble Somatic Variant Merging and Masking: Encyclopedia/pages/Aliquot_Ensemble_Somatic_Variant_Merging_and_Masking.md
- Analyte: Encyclopedia/pages/Analyte.md
- Annotations: Encyclopedia/pages/Annotations.md
- Annotations TCGA: Encyclopedia/pages/Annotations_TCGA.md
- Arriba: Encyclopedia/pages/Arriba.md
- ASCAT2: Encyclopedia/pages/ASCAT2.md
- ASCAT3: Encyclopedia/pages/ASCAT3.md
- AscatNGS: Encyclopedia/pages/AscatNGS.md
- BCGSC miRNA Profiling: Encyclopedia/pages/BCGSC_miRNA_Profiling.md
- Biospecimen Data: Encyclopedia/pages/Biospecimen_Data.md
- Birdseed: Encyclopedia/pages/Birdseed.md
- BRASS: Encyclopedia/pages/BRASS.md
- Cancer Genomics Hub: Encyclopedia/pages/Cancer_Genomics_Hub.md
- Case: Encyclopedia/pages/Case.md
- Center for Cancer Genomics: Encyclopedia/pages/Center_for_Cancer_Genomics.md
- Clinical Data: Encyclopedia/pages/Clinical_Data.md
- Clinical Supplement: Encyclopedia/pages/Clinical_Supplement.md
- Controlled Access: Encyclopedia/pages/Controlled_Access.md
- Data Access Policy: Encyclopedia/pages/Data_Access_Policy.md
- Data Submitter: Encyclopedia/pages/Data_Submitter.md
- dbGaP: Encyclopedia/pages/dbGaP.md
- Entity: Encyclopedia/pages/Entity.md
- FM Simple Somatic Mutation: Encyclopedia/pages/FM_Simple_Somatic_Mutation.md
- FoundationOne Annotation: Encyclopedia/pages/FoundationOne_Annotation.md
- FoundationOne Variant Aggregation and Masking: Encyclopedia/pages/FoundationOne_Variant_Aggregation_and_Masking.md
- FPKM-UQ: Encyclopedia/pages/FPKM-UQ.md
- FPKM: Encyclopedia/pages/FPKM.md
- GATK4 MuTect2 Tumor-Only: Encyclopedia/pages/GATK4_MuTect2_Tumor-Only.md
- GATK4 MuTect2 Tumor-Only Annotation: Encyclopedia/pages/GATK4_MuTect2_Tumor-Only_Annotation.md
- GDC API: Encyclopedia/pages/GDC_API.md
- GDC Data Portal: Encyclopedia/pages/GDC_Data_Portal.md
- GDC Data Submission Portal: Encyclopedia/pages/GDC_Data_Submission_Portal.md
- GDC Data Transfer Tool: Encyclopedia/pages/GDC_Data_Transfer_Tool.md
- GDC Documentation Site: Encyclopedia/pages/GDC_Documentation_Site.md
- GDC Web Site: Encyclopedia/pages/GDC_Web_Site.md
- Genomic Data Analysis Network: Encyclopedia/pages/Genomic_Data_Analysis_Network.md
- Genomic Data Commons: Encyclopedia/pages/Genomic_Data_Commons.md
- Harmonized Data: Encyclopedia/pages/Harmonized_Data.md
- Latest Data: Encyclopedia/pages/Latest_Data.md
- Manifest File: Encyclopedia/pages/Manifest_File.md
- MD5 Checksum: Encyclopedia/pages/MD5_Checksum.md
- MuSE: Encyclopedia/pages/MuSE.md
- MuSE Annotation: Encyclopedia/pages/MuSE_Annotation.md
- Mutation Annotation Format: Encyclopedia/pages/Mutation_Annotation_Format.md
- Mutation Annotation Format TCGAv2: Encyclopedia/pages/Mutation_Annotation_Format_TCGAv2.md
- MuTect2: Encyclopedia/pages/MuTect2.md
- MuTect2 Annotation: Encyclopedia/pages/MuTect2_Annotation.md
- Pindel: Encyclopedia/pages/Pindel.md
- Pindel Annotation: Encyclopedia/pages/Pindel_Annotation.md
- Redaction: Encyclopedia/pages/Redaction.md
- Release Number: Encyclopedia/pages/Release_Number.md
- REST API: Encyclopedia/pages/REST_API.md
- RNA-Seq: Encyclopedia/pages/RNA-Seq.md
- SeSAMe Methylation Beta Estimation: Encyclopedia/pages/SeSAMe_Methylation_Beta_Estimation.md
- Seurat 10x Chromium: Encyclopedia/pages/Seurat_10x_Chromium.md
- SNP Array-Based Data: Encyclopedia/pages/SNP_Array-Based_Data.md
- STAR-Fusion: Encyclopedia/pages/STAR-Fusion.md
- STAR 2-Pass Chimeric: Encyclopedia/pages/STAR_2-Pass_Chimeric.md
- STAR 2-Pass Genome: Encyclopedia/pages/STAR_2-Pass_Genome.md
- STAR 2-Pass Transcriptome: Encyclopedia/pages/STAR_2-Pass_Transcriptome.md
- STAR Counts: Encyclopedia/pages/STAR_Counts.md
- TCGA Barcode: Encyclopedia/pages/TCGA_Barcode.md
- TCGA VCF 1.1v2: Encyclopedia/pages/TCGA_VCF_1.1v2.md
- TCIA: Encyclopedia/pages/TCIA.md
- UUID: Encyclopedia/pages/UUID.md
- Variant Call Format: Encyclopedia/pages/Variant_Call_Format.md
- Variant Type: Encyclopedia/pages/Variant_Type.md
- VarScan2: Encyclopedia/pages/VarScan2.md
- VarScan2 Annotation: Encyclopedia/pages/VarScan2_Annotation.md
- VCF LiftOver: Encyclopedia/pages/VCF_LiftOver.md
site_name: GDC Docs
site_url: https://docs.gdc.cancer.gov
theme:
custom_dir: overrides
favicon: images/favicon.ico
features:
- navigation.tabs
- navigation.tabs.sticky
logo: images/nih-header-logo-color.png
name: material
palette:
primary: white
scheme: gdc-accessible
plugins:
- search