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DPIPE Documentation

sv-pack release notes

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
- 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 sv-pack release notes
    Table of contents
    
    Version v1.3.0
    
    Version v1.2.0
    
    Version v1.1.0
    
    Version v1.0.0
    
    Changes
    
    Version v0.9.0
  - 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

Release notes

Version v1.3.0

Introduce better functionality for making custom filters
Changes to utils
Allow the "search" relation to filters for doing regex search. Primarily meant for crude searching in the CSQ from VEP. Splitting on , and and require regex to match all parts.
Changes to sv_postprocessing allow checking for existence of INFO-fields and setting filter exceptions.

Version v1.2.0

Introduce more flexible filtering definitions
Changes to standardization
Ensure minimal starting position is base 1
Add CN from Canvas to the FORMAT field when Canvas is merged with Manta

Version v1.1.0

Rescue ACMG_class 4,5 and add ACMG_class column to TSV output

Version v1.0.0

Changes

Breaking change

Removes the --print-argument from the Python scripts

New features

Directly installs runnable scripts
sv_standardizer
sv_postprocessing
sv_wgs_filtering
Moves parsing and formatting of VCFs into src/sv_utils.py
Remove non-variants (DRAGEN:REF)
Add INFO fields canvasSM, canvasPE, canvasBC to back up FORMAT fields SM, PE, BC. Useful for merging.

Version v0.9.0

Version v0.9.0 of this repository was never released, but is a collection of the Python scripts hardcoded in the following repositories

svtools@v0.1.2
anno-targets@74a1b0f8a4f7045b8e8a628d059c2c0927e558d3