GAIn: Genomics Annotation Infrastructure

Overview

GAIn Documentation

• GAIn Getting started on the web
• Getting started on CLI
  • Installation
  • Check available resources (grr_browse)
  • Create your first GRR (grr_create)
  • Select GRR to work with
  • Simple_annotation_pipeline
  • Annotate_columns
  • Annotate_vcf
  • Parallelization
  • Reannotation
  • Annotating CNVs, regions, positions
• Getting started with GRR tutorial
• Genomic resources
  • genomic_resource.yaml
  • Types of genomic resources and their configurations
    • Genomic scores
    • Gene models
    • Reference genome
    • Liftover chain
    • Annotation pipeline
  • Histograms and statistics
    • Histograms
    • Number Histograms Configuration
    • Categorical Histograms Configuration
    • Null Histograms Configuration
• Resource repositories
  • Repository discovery
  • Repository configuration
  • Caching of repositories
  • Management of resources and repositories with CLI tools
    • grr_manage
    • grr_browse
• Tutorial: Create a local repository with a custom resource
  • Create an empty GRR
  • Create an empty genomic resource
    • Add genomic score resources
• Genomic position table configuration
• Table configuration fields
• Score configuration fields
• Auto generated score definition
• Zero-based / BED format scores
• Example configurations
• How to generate tabix files
  • Example usage of tabix
• Annotation Infrastructure
  • Pipeline configuration
  • Preamble
  • Annotators
    • Annotator attribute fields
    • Score annotators
    • Effect annotator
    • Simple effect annotator
    • Liftover annotator
    • Normalize allele annotator
    • Chromsome mapping annotator
    • Gene score annotator
    • Gene set annotator
    • SpliceAI annotator plugin
    • VEP annotators
  • Command line tools
    • Notes on usage
    • annotate_columns
    • annotate_vcf
    • annotate_schema2_parquet
    • annotate_doc
  • Example annotations
    • How to annotate variants with ClinVar
    • How to annotate with gene score annotators
    • Gene score annotator with changed aggregator
    • How to annotate with gene set annotators
    • Simple position score annotation
    • Effect annotator with default resources
    • Liftover annotation
• GAIn Web interface
• Annotators Plugin Library
• GAIn Python Interface