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DPIPE Documentation

Status for GDx-bioinf systems

DPIPE Documentation

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Organization
Organization
- Bioinformatics group roles
- Overall process of work organisation
Procedures
Procedures
- Onboarding
  Onboarding
- Production
  Production
  - Production routines
    Production routines
    
    Execution and monitoring of production pipelines
    
    Scheduled recurring jobs
    
    Running annoservice
    
    ELLA daily operations
    
    ELLA core production and maintenance
    
    Using service user
    
    Use of GDx operational channel in Teams
    
    User accounts management
    
    VardeDB manual procedures
  - Helpdesk routines
    Helpdesk routines
    
    GDx-bioinf Service Level Agreement
    
    GDx-bioinf helpdesk user page
    
    GDx-bioinf helpdesk process
  - Annotation and reference data updates
    Annotation and reference data updates
    
    Update of external annotation data
    
    Update of in-house annotation data
    
    Update of CoNVaDING background data
    
    Generating IGV tracks for CNV annotations
  - Releases and production system updates
    Releases and production system updates
    
    Updates to production pipelines
    
    Release and deployment of TSD import
    
    Release and deployment of vcpipe
    
    Release and deployment of anno system
    
    Using the vcpipe staging environment
  - Capture regions and gene panels configuration
    Capture regions and gene panels configuration
    
    Create region files for new capture kits
    
    Design and build gene panels
    
    Export and deploy gene panels
    
    Update external reference data for the gene panel builder
- Development
  Development
  - Status for GDx-bioinf systems Status for GDx-bioinf systems
    Table of contents
    
    Core production systems
  - In-house databases and CNV in panels
  - Software development and review
  - Issue management
  - System owner checklist
  - How to start a new Gitlab project repo
Specifications and repo documentation
Specifications and repo documentation
- Systems and infrastructure
  Systems and infrastructure
- Production pipelines and automation
  Production pipelines and automation
  - Maestro library for pipeline automation
  - Steps implementention of Maestro
  - Demultiplexing and QC of raw seq data (NSC)
  - Basepipe pipeline
  - Triopipe pipeline
  - CNV exome targeted
  - TSD import (tsd-import)
    TSD import (tsd-import)
    
    TSD import and LIMS integration (tsd-import)
    
    tsd-import release notes
- Variant calling
  Variant calling
  - Variant calling pipeline (vcpipe)
    Variant calling pipeline (vcpipe)
    
    Variant calling pipeline (vcpipe)
    
    vcpipe architecture
    
    vcpipe automation: executor
    
    vcpipe webUI
    
    vcpipe pipelines
    
    vcpipe test datasets
    
    vcpipe reference datasets
    
    vcpipe release notes
  - CNV calling in targeted gene panels (CoNVaDING)
  - Noninvasive prenatal testing (NIPT)
    Noninvasive prenatal testing (NIPT)
    
    NIPT
    
    NIPT hardware and IT infrastructure
    
    NIPT repository
- Annotation and post-processing
  Annotation and post-processing
  - Anno and anno-targets
    Anno and anno-targets
    
    Anno with anno-targets
    
    Annopipe
    
    Anno official documentation
  - Post-processing and filtering of structural variants and CNVs
    Post-processing and filtering of structural variants and CNVs
    
    CNV filtering
    
    Post-processing of structural variants (sv-pack)
    
    sv-pack release notes
  - SNV filtering upstream of ELLA
- Interpretation
  Interpretation
  - ELLA: clincical variant interpretation
    ELLA: clincical variant interpretation
    
    ELLA official documentation
    
    ELLA official home page
  - Gene panel builder (GPB)
    Gene panel builder (GPB)
    
    Gene panel builder
    
    User manual
    
    Release notes
    
    Background
    Background
    
    About gene panels
    
    Technical implementation
    
    Set up for production
    Set up for production
    
    Deploying to production
    
    Authentication and autorization
    
    Command-line interface
    
    Coverage and segmental duplications
    
    Set up for development
    Set up for development
    
    Development
    
    Demo deployment
- Data sharing
Documentation
Documentation
- About our documentation
- docs-builder (for docs webpages)
- docs-store (for docs not in other repos)
- Procedures for updating eHåndbok and docs
  Procedures for updating eHåndbok and docs
  - How to update eHåndbok (EHB)
  - How to update docs webpages

Status for GDx-bioinf systems

Core production systems

The table below lists the latest release for important source code repositories. Follow the links for previous releases.

System	Repository	Version
Automation	TSD import and LIMS integration (tsd-import)
Automation	Maestro	[none]
Automation	Steps	[none]
Variant calling	Variant calling pipeline (vcpipe)
Variant calling	Non-invasive prenatal testing (NIPT)	[none]
Annotation	ella-anno
Annotation	anno-targets
Annotation	Post-processing of structural variants (sv-pack)
Interpretation	ELLA
Interpretation	Gene panel builder (GPB)
Interpretation	Gene panel store