GPF: Genotypes and Phenotypes in Families documentation

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 Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform for a detailed description.

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

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
• Users
  • How to create a new user?
  • How to specify permissions for a given user?
  • Reset password
  • Delete user
  • Edit user name
• Groups
  • Special Groups
  • Creating group
  • Adding users and dataset to group
• Dataset access
  • 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
  • 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
    • annotate_schema2_parquet
  • 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
• GPF Development
  • Release Notes
  • gpf package
    • Subpackages
    • Module contents
  • gpf_web package
    • Routes
    • Subpackages