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Organization
Organization
Bioinformatics group roles
Project management and agile
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 anno
ELLA production routines
ELLA core production routines
Use of service user
User accounts management
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 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
Development and review
Issue management
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
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
README
See
Coverage and Segmental Duplications
.
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