GPF Administration

• GPF Getting Started Guide
  • Setup
  • Importing genotype data
  • Getting Started with Annotation
  • Getting Started with Phenotype Data
  • Getting Started with Preview Columns
  • Example import of real de Novo variants
  • Example import of real CNV variants
  • Example import of real phenotype data
  • Getting Started with Gene Sets and Gene Scores
  • Getting Started with Enrichment Tool
  • Getting Started with Gene Profiles
  • Getting Started with Federation
  • Example Usage of GPF Python Interface
• Genomic resources and resource repositories
  • Genomic resources
  • Resource repositories
  • Tutorial: Create a local repository with a custom resource
• 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
• Annotation Infrastructure
  • Pipeline configuration
  • Preamble
  • Annotators
  • Command line tools
  • Example annotations
• Working With Pedigree Files Guide
  • Brief outline
  • Input pedigree file
  • Canonical pedigree file
  • Possible input pedigree file structures
  • Preparing the pedigree data
  • Supported values for sex
  • Supported values for status
  • Supported values for role
  • Common arguments for the pedigree tools
  • Transform a pedigree file into canonical GPF form
  • Visualize a pedigree file into a PDF file
• Working With VCF Files Guide
  • Import data from the “1000 Genome Project”
  • Creating the pedigree file
  • Creating the VCF files
  • Importing the data into GPF
• Phenotype Database Tools
  • Importing via import project configuration
  • Importing via pheno_import tool
  • Building the phenotype browser database
  • The instrument dictionary file
  • The data dictionary file
  • Updating instrument and measure descriptions in existing databases
  • Measure classification
  • Measure histogram configurations
• Measure Configuration
  • Measure configuration format
• GPF Tools
  • Simple Study Import
  • Impala Batch Import
  • Generate Denovo Gene Sets
  • Generate Common Report
  • Import Tools
• GPF Instance Configuration
• GPF Study Configuration
• Publicly Accessible GPF Site
  • Requirements for the host
  • DNS name
  • Firewall
  • Required Software
  • SSL Certificate
  • Create an installation user
  • Directory Structure
  • GRR Definition File
  • GPF Instance Directory
  • GPF Docker Compose File
  • Start GPF
  • Create GPF Admin User and OAuth2 Application
  • Apache2 Proxy Configuration
• Data Appendix
  • Gene Weights
  • Genomic Scores
  • Columns