GPF: Genotypes and Phenotypes in Families

• GPF User Interface
  • Dataset Description
  • Dataset Statistics
    • Families by number
    • Families by pedigree
    • De Novo variants
  • Gene Browser
  • Genotype Browser
  • Phenotype Browser
  • Enrichment Tool
  • Phenotype Tool
  • Gene Profiles
    • Gene Profiles - single view
  • Filters
    • General Filters
    • Gene symbols filter
    • Gene sets filter
    • Gene scores
    • Regions filter
    • Study filters
    • Genomic scores filters
    • Family and person filters
    • Unique family variants
• GPF Administration
  • GPF Getting Started Guide
    • Prerequisites
    • GPF Installation
    • Run the GPF development web server
    • Import genotype variants
    • Getting started with Dataset Statistics
    • Getting started with de novo gene sets
    • Getting Started with Annotation
    • Getting Started with Preview and Download Columns
    • Getting Started with Gene Browser
    • Getting Started with Enrichment Tool
    • Getting Started with Phenotype Data
    • Using Apache Impala as storage
    • 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
    • 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
    • Import a Phenotype Database
    • The Data Dictionary
    • Measure Classification
    • Inference parameters
    • How The Classification Works
  • Measure Configuration
    • Measure configuration format
  • GPF Tools
    • Simple Study Import
    • Impala Batch Import
    • Generate Denovo Gene Sets
    • Generate Common Report
    • Import Tools
  • Data Appendix
    • Gene Weights
    • Genomic Scores
    • Columns
• GPF Development
  • Release Notes
  • dae Interface
    • Genomic Resources
    • Annotation
    • Effect Annotation
    • Genomic Variants
    • Pedigrees Tools
    • Variants Loaders
    • Import Tools
    • Genotype Data Parquet Writers
    • Query Genomic Variants
    • Genotype Storage
    • In-Memory Genotype Storage
    • Impala Genotype Storages
    • Configuration
    • Genotype Data
    • Phenotype Data
    • Phenotype tool
    • Enrichment Tool
    • Gene Properties
    • Tools
  • wdae Interface
    • Common reports api
    • Datasets api
    • Enrichment api
    • Family api
    • Gene scores
    • Gene sets
    • Gene view
    • Genomes api
    • Genomic scores api
    • Genotype browser
    • Gpf instance
    • Groups api
    • Measures api
    • Person sets api
    • Pheno browser api
    • Pheno tool api
    • Query state save
    • Sentry
    • User queries
    • Users api
    • genotype_browser package
    • users_api package