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DPIPE Documentation
Home
Organization
Organization
Bioinformatics group roles
Overall process of work organisation
Procedures
Procedures
Onboarding
Onboarding
Employee onboarding
Training for running pipeline
Training for ELLA core developers
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 requests
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 ELLA track config manager
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
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
Systems overview
Infrastructure
Storage and security of sensitive data
File system usage and locations
Software administration
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
Preimplementation Genetic Testing (PGT)
Preimplementation Genetic Testing (PGT)
PGT 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
ELLA CNV module backend
CNV filtering
Post-processing of structural variants (sv-pack)
sv-pack release notes
SNV filtering upstream of ELLA
Interpretation
Interpretation
ELLA: clinical variant interpretation
ELLA: clinical variant interpretation
ELLA official documentation
ELLA official home page
ELLA CNV module frontend
ELLA MT report
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
File system usage and locations
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