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DPIPE Documentation

Gene panel builder

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
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
    Maestro library for pipeline automation
    
    Maestro
    
    Setting up Maestro
    
    Technical documentation
    
    Maestro UI user manual
  - 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 Gene panel builder
    Table of contents
    
    Documentation
    
    User manual and release notes
    
    Background
    
    Set up for production
    
    Set up for development
    
    Contact
    
    License and copyright
    
    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

Gene panel builder

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Gene panel builder

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Gene panel builder (GPB) is a companion utility for genetic variants interpretation software such as ELLA to build virtual gene panels with transcript information and inheritance modes, with coverage information from your pipeline as an aid in the process.

Documentation

Built docs available at DPIPE Documentation. See also our GitLab repository.

User manual and release notes

User manual: How-to for GPB end users.
Release notes: Versions and changes.

Background

About gene panels: Why do we need gene panels and a tool such as GPB?
Technical implementation: A brief high-level overview of GPB's technical implementation

Set up for production

Production deployment: How to set up GPB in a production environment.
Authentication and authorization: Explanation of how GPB handles authentication, including how to disable it in the production environment, if necessary.
Coverage and segmental duplications: How to create files for coverage and segmental duplications, and configure how these are displayed in the frontend.
Command line interface: CLI for common tasks.

Set up for development

Development: Set up GPB in a development environment.
Demo deployment: Set up a public demo instance of GPB.

Contact

For support and suggestions, please contact ella-support.

License and copyright

Gene panel builder (GPB) Copyright (C) 2022-2024 GPB contributors

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.