GPF: Genotypes and Phenotypes in Families

GPF (Genotypes and Phenotypes in Families) is an open-source platform that manages genotypes and phenotypes derived from collections of families. The GPF interface allows interactive exploration of genetic variants, enrichment analysis for de novo mutations, and phenotype/genotype association tools. In addition, GPF allows researchers to share their data securely with the broader scientific community. See the The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI for a detailed description.

GPF is an open-source project available at GitHub developed by Iossifov’s group at CSHL and Seqpipe Ltd, Sofia, Bulgaria.

GPF is deployed at the Simons Foundation (https://gpf.sfari.org), providing protected access to comprehensive genotypic and phenotypic data for the SSC, SPARK, and related datasets.

Tutorial videos

• short: https://youtu.be/6G_woic72Qk

• long: https://youtu.be/-4-bF08JiR8

GPF Documentation

• GPF User Interface
  • Dataset Description
  • Dataset Statistics
    • Families by number
    • Families by pedigree
    • De Novo variants
  • Gene Browser
  • Genotype Browser
  • Phenotype Browser
  • Enrichment Tool
    • Background models
  • 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 User Management
    • How to create a new user?
    • How to specify permissions for a given user?
    • Reset password
    • Delete user
    • Edit user name
    • Special Groups
    • Creating group
    • Adding users and dataset to group
    • Adding group to a dataset
• 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
• 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