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Genomics England Research Environment User Guide

Release V7 (25/07/2019)

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Getting started
How-to guides
Data
Desktop applications
CloudOS
High Performance Cluster (HPC)
Workflows and scripts
Getting help
Data security and Export
Training

Genomics England Research Environment User Guide

Home
Getting started
Getting started
- Welcome pack
- Accessing the RE
  Accessing the RE
- Learning to use the RE
- Your role as a researcher
  Your role as a researcher
- Files, directories and import/export
  Files, directories and import/export
- Technical information
  Technical information
How-to guides
How-to guides
- Complete end-to-end guides
  Complete end-to-end guides
- Working with the desktop applications (videos)
  Working with the desktop applications (videos)
- Data exploration
  Data exploration
  - Working with LabKey
    Working with LabKey
    
    Labkey API
    
    Labkey API configuration
    
    Working with NHS GMS data within LabKey
    
    Labkey videos
  - Getting medical histories
    
    Getting medical histories
    
    Accessing and comparing medical history data with Participant Explorer
    
    Accessing medical history data programmatically
    
    Accessing mental health data programmatically
- Cohort building
  Cohort building
  - Phenotype-first cohort building
    
    Phenotype-first cohort building
    
    Building cohorts with Participant Explorer
    
    Building cohorts with Cohort Browser in CloudOS
    
    Building cancer cohorts programmatically
    
    Building rare disease cohorts programmatically
  - Genotype-first cohort building
    
    Genotype-first cohort building
    
    Using our variant screening workflows
    
    Finding participants by genotype in IVA
    
    Finding participants by genotype in Cohort browser in CloudOS
    
    Finding participants with prioritised variants programmatically
    
    Querying aggregate VCF files to find participants by genotypes
- Working with our aggregate VCF datasets
  Working with our aggregate VCF datasets
- Task FAQs
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
- Genomic data sources
- Transcriptomics pilot data
- Research study cohort data
  Research study cohort 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
    
    Summary statistics across genetically-inferred ancestry groups for 100,000 Genomes Project participants
    
    AggV2 allele frequencies
    
    AggV2 Principal components and genetically inferred relatedness
    
    AggV2 Ancestry inference
    
    AggV2 file manifest
    
    AggV2 FAQs
  - Somatic aggregated variant calls
    
    Somatic aggregated variant calls
    
    somAgg sample stats
    
    somAgg variant counts per chunk
    
    somAgg VCF aggregation
  - 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 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 19
    
    Cancer staging statistics 18
    
    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
    
    ONT cancer pilot project
    
    ONT rare disease
    
    PacBio rare disease pilot
    
    ONT pilot
    
    ONT COVID-19
  - Orthogonal standard-of-care (SOC) test data (cancer)
  - 100,000 Genomes Cancer Programme - pan-cancer publication
  - Clinical application of tumour in normal contamination assessment from WGS - TINC 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 4 (22/08/2024)
    
    Release 3 (18/03/2024)
    
    Release 2 (28/02/2023)
    
    Release 1 (15/06/2022)
  - 100kGP (main programme) releases
    
    100kGP (main programme) releases
    
    Change summary
    
    Release 19 (31/10/2024)
    
    Release 18 (21/12/2023)
    
    Release 17 (30/03/2023)
    
    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 v7.0
    
    COVID-19 data release v6.0
    
    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
- RStudio
- 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
- BioMart
- Terminal application
- Jupyter notebooks
- VSCode
- LibreOffice
CloudOS
CloudOS
- CloudOS data
High Performance Cluster (HPC)
High Performance Cluster (HPC)
- What is an HPC?
- Accessing the HPC
- How to run jobs on the HPC
  How to run jobs on the HPC
- Using software on the HPC
- How to request software installation within the Research Environment
- Using R on the HPC
  Using R on the HPC
- Python packages and personal conda environments
- Importing software with containers
  Importing software with containers
  - Step-by-step guide to using containers
  - Troubleshooting with containers
- Jupyter Lab on the HPC
Workflows and scripts
Workflows and scripts
- Workflows
  Workflows
  - Association testing
    Association testing
    
    Aggregate variant testing (AVT)
    
    Aggregate variant testing (AVT)
    
    Input files
    
    Parameters
    
    Output files
    
    Known issues and limitations
    
    Changelog
    
    Previous WDL versions
    Previous WDL versions
    
    v3
    
    v3
    
    AVT detailed input file overview
    
    GWAS
    
    GWAS
    
    Version history
    
    Optional arguments and default
    
    Detailed process output
    
    Software versions
    
    Common errors
  - Variant screening
    Variant screening
    
    Small Variant
    
    Small Variant
    
    Parameters
    
    Input files
    
    Output files
    
    Known issues and limitations
    
    Changelog
    
    Previous WDL version
    Previous WDL 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
- Scripts
  Scripts
  - Extract variants by coordinate
  - Cancer survival analysis
  - Somatic SVs and CNVs for a specific gene
  - Variant Effect Predictor (VEP)
    
    Variant Effect Predictor (VEP)
    
    VEP container for older releases
- Support
Getting help
Getting help
Data security and Export
Data security and Export
- Data security and you
- Airlock - importing and exporting files
  Airlock - importing and exporting files
- Reporting potential diagnoses and contacting clinicians
  Reporting potential diagnoses and contacting clinicians
  - Clinical Research Interface FAQs
Training
Training

100kGP Release V7 (25/07/2019)¶

Data dictionary

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