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DPIPE Documentation

Systems overview

DPIPE Documentation

Home
Organization
Organization
- Bioinformatics group roles
- Project management and agile
Procedures
Procedures
- Onboarding
  Onboarding
- Production
  Production
  - Production routines
    Production routines
    
    Execution and monitoring of production pipelines
    
    Scheduled recurring jobs
    
    Running anno
    
    ELLA production routines
    
    ELLA core production routines
    
    Use of service user
    
    User accounts management
  - Annotation and reference data updates
    Annotation and reference data updates
    
    Update of public annotation data
    
    Update of sensitive 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 and anno-targets
    
    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
Specifications and repo documentation
Specifications and repo documentation
- Systems and infrastructure
  Systems and infrastructure
  - Systems overview Systems overview
    Table of contents
    
    High-level bioinformatics production workflow
    
    Detailed bioinformatics production workflow
    
    System landscape
    
    Lab automation
    
    vcpipe
    
    Annotation
  - Infrastructure
  - Storage and security of sensitive data
  - File system usage and locations
  - Software administration
- Production pipelines and automation
  Production pipelines and automation
  - Demultiplexing and QC of raw seq data (NSC)
  - Basepipe
  - Triopipe
  - 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 targetet gene panels (CoNVaDING)
  - Noninvasive prenatal testing (NIPT)
    Noninvasive prenatal testing (NIPT)
    
    NIPT
    
    NIPT hardware and 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
    
    Production deployment
    
    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

Systems overview

This document collects overview diagrams of our systems (workflow and C4 diagrams). This will be changing as the system landscape changes with ongoing projects.

High-level bioinformatics production workflow

high-level-flow

Detailed bioinformatics production workflow

System landscape

system_landscape

Lab automation

vcpipe

vcpipe containers

Annotation

annotation containers