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Genomics England Research Environment User Guide

Release V7 (25/07/2019)

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Getting started
Data
Desktop applications
Cloud-RE
High Performance Cluster (HPC)
Workflows, scripts and containers
Getting help
Data security and you
Tutorials

Genomics England Research Environment User Guide

Home
Getting started
Getting started
- Welcome pack
- Accessing the TRE
  Accessing the TRE
  - Setting up AWS
  - Accessing the RE FAQs
- Learning to use the TRE
- What are you trying to do in the Research Environment?
  What are you trying to do in the Research Environment?
- Your role as a researcher
  Your role as a researcher
  - Introduction to the GECIP
  - Student guidelines
- Files, directories and import/export
  Files, directories and import/export
- Technical information
  Technical information
Data
Data
- Data overview
  Data overview
- 100kGP disease models
- Clinical and phenotype data
  Clinical and phenotype data
  - 100kGP clinical and phenotype data
    
    100kGP clinical and phenotype data
    
    Cancer-specific 100kGP clinical data
    
    Rare disease-specific 100kGP clinical data
    
    General 100kGP clinical data
  - NHS Genomic Medicine Service (GMS) Clinical and Phenotype data
    
    NHS Genomic Medicine Service (GMS) Clinical and Phenotype data
    
    Cancer-specific NHS GMS clinical data
    
    Rare disease-specific NHS GMS clinical data
    
    General NHS GMS clinical data
  - COVID-19 clinical data
- Genomic data
- Genomics England bioinformatics data
  Genomics England bioinformatics data
  - Aggregated variant calls(AggV2)
    
    Aggregated variant calls(AggV2)
    
    AggV2 details
    AggV2 details
    
    AggV2 sample QC
    
    AggV2 gVCF aggregation
    
    AggV2 variant normalisation and representation
    
    AggV2 site QC, FILTER and INFO Fields
    
    AggV2 functional annotation
    
    AggV2 allele frequencies
    
    AggV2 Principal components and genetically inferred relatedness
    
    AggV2 Ancestry inference
    
    AggV2 file manifest
    
    AggV2 code book
    
    AggV2 code book
    
    AggV2 code book general information
    
    AggV2 code book genotype queries
    
    AggV2 code book functional annotation queries
    
    AggV2 code book phenotype queries
    
    AggV2 code book combining queries
    
    AggV2 FAQs
  - Somatic aggregated variant calls
    
    Somatic aggregated variant calls
    
    somAgg sample stats
    
    somAgg variant counts per chunk
    
    somAgg VCF aggregation
    
    somAgg code book
    
    somAgg code book
    
    somAgg code book general information
    
    somAgg code book genotype queries
    
    somAgg code book functional annotation queries
    
    somAgg code book phenotype queries
  - COVID-19 aggregations
    
    COVID-19 aggregations
    
    COVID-19 aggregation methods
    
    Data available for the COVID-19 aggregation
    
    COVID-19 publication
  - Genetic similarity to worldwide populations (ancestry) in the UK Biobank
  - De novo variant research dataset
    
    De novo variant research dataset
    
    Where and how to access de novo data
    
    De novo data cohort statistics
    
    De novo data code book
    
    De novo data FAQs
  - Tiering
    Tiering
    
    Rare disease tiering
    
    Cancer tiering
    
    Interpretation request (rare disease)
  - Solved cases (rare disease)
  - HLA variants
  - Exomiser
  - Cancer analysis
    Cancer analysis
    
    Cancer analysis
    
    Cancer analysis histology and TGCA study
  - Staging data (cancer)
    
    Staging data (cancer)
    
    Cancer staging statistics 17
    
    Cancer staging statistics 16
    
    Cancer staging statistics 15
    
    Cancer staging statistics 14
    
    Cancer staging statistics 13
    
    Cancer staging statistics 12
    
    Cancer staging statistics 11
    
    Cancer staging statistics 10
    
    Cancer staging statistics 9
    
    Cancer staging statistics 8
  - Long-read sequencing data
    
    Long-read sequencing data
    
    Long-read genomic data from ONT
    
    Long-read genomic data from PacBio (Pilot)
    
    COVID-19 long read sequencing
  - Orthogonal standard-of-care (SOC) test data (cancer)
  - 100,000 Genomes Cancer Programme - pan-cancer publication
- Publicly available data
- Research community provided data
  Research community provided data
- Data releases
  Data releases
  - Genomic Medicine Service (GMS) data releases
    
    Genomic Medicine Service (GMS) data releases
    
    Change summary
    
    Release 1 (15/06/2022)
  - Main programme releases
    
    Main programme releases
    
    Change summary
    
    Release 16 (13/10/2022)
    
    Release 15 (26/05/2022)
    
    Release 14 (27/01/2022)
    
    Release 13 (30/09/2021)
    
    Release 12 (06/05/2021)
    
    Release 11 (17/12/2020)
    
    Release 10 (03/09/2020)
    
    Release 9 (02/02/2020)
    
    Release 8 (28/11/2019)
    
    Release 7 (25/07/2019)
    
    Release 6 (28/02/2019)
    
    Release 5.1 (20/11/2018)
    
    Release 5 (31/10/2018)
    
    Release 4 (31/07/2018)
    
    Release 3 (20/04/2018)
    
    Release 2 (30/01/2018)
    
    Release 1 (11/10/2017)
  - Covid-19 data releases
    
    Covid-19 data releases
    
    COVID-19 data release v5.0
  - Frequent data releases
- Application data versions
- Terminology server
Desktop applications
Desktop applications
- LabKey - tables of data
  LabKey - tables of data
- R in the Research Environment
  R in the Research Environment
  - R, RStudio, and R libraries
  - Using Rstudio on the HPC
    Using Rstudio on the HPC
    
    Enable the terminal in Rstudio
    
    Change keyboard shortcut
    
    Logging into the HPC, and setting up your environment
    
    Additional configuration and caveats
  - Self-service R package installation
- Data Discovery - understand the cohort
  Data Discovery - understand the cohort
- Participant Explorer - search for participants
  Participant Explorer - search for participants
- Interactive Variant Analysis (IVA) - catalogue of variants
  Interactive Variant Analysis (IVA) - catalogue of variants
- Integrative Genome Viewer (IGV) - visualise genomic data
- PanelApp - curated gene lists
- Airlock - importing and exporting files
  Airlock - importing and exporting files
- BioMart
- Terminal application
- Jupyter notebooks
- VSCode
  VSCode
  - Installing VSCode Extensions
  - Python development in VSCode
- LibreOffice
- Rocket chat - communicate with other RE users
Cloud-RE
Cloud-RE
- CloudOS data
High Performance Cluster (HPC)
High Performance Cluster (HPC)
Workflows, scripts and containers
Workflows, scripts and containers
- Workflows
  Workflows
  - Association testing
    Association testing
    
    Aggregate variant testing (AVT)
    
    Aggregate variant testing (AVT)
    
    AVT detailed input file overview
    
    Previous versions of AVT
    
    Previous versions of AVT
    
    AVT v2
    
    AVT v2
    
    Aggregate Variant Testing "input variables" file
    
    Aggregate Variant Testing example use cases
    
    AVT v1
    
    AVT v1
    
    Aggregate Variant Testing Inputs File
    
    GWAS
    
    GWAS
    
    Version history
    
    Optional arguments and default
    
    Detailed process output
    
    Software versions
    
    Common errors
  - Variant screening
    Variant screening
    
    Small Variant
    
    Small Variant
    
    Small variant workflow changelog
    
    Small variant workflow appendix
    
    Previous version
    Previous version
    
    v1
    
    v1
    
    Troubleshooting the Gene Variant workflow
    
    Structural Variant
    
    Structural Variant
    
    Structural variant workflow changelog
    
    Structural variant workflow appendix
    
    Previous versions
    Previous versions
    
    v2.0.1
    
    v2.0.1
    
    v1.2
    
    Functional Annotation
- Scripts
  Scripts
- Support
Getting help
Getting help
Data security and you
Tutorials
Tutorials

data reference

Release V7 (25/07/2019)¶

Data dictionary

Last update: November 3, 2023

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