Welcome to the GPAP Documentation

CONTENTS

• Getting started
• Phenotypic Data
  • Submission of phenotypic data
    • New Index Case
    • Import Cases
    • New Family Member
    • Edit Pedigree
    • Assign Participant Permissions
    • Update newly solved cases
    • External Resources
  • Management of phenotypic data
    • Browse GPAP PhenoStore Cases
    • Export GPAP Phenostore Cases
• Experiment Data
  • Data Submission
    • Submit Experiment Metadata
    • Submit File Metadata
    • Upload sequencing files through RedIris server
  • Data Management
    • Experiments
    • Files
    • Statistics on Experiment Access
    • Experiment Analysis Status
    • Experiment QC Metrics
• Genomic Analysis
  • Study setup
    • Case Analysis
      • 1. Select experiments
      • 2. Review case information
      • 3. Select inheritance mode
        • Quality Settings
      • 4. Apply filters
    • Cohort Analysis
      • 1. Select a Cohort
      • 2. Select genotype:
      • 3. Select Genes:
      • 4. Apply variant filters:
    • Search Across All Experiments
      • 1. Select genotype
      • 2. Select genes
      • 3. Apply variant filters
  • Filtering
    • Predefined filter set
    • Variant Filters
      • Variant Type:
      • Population:
      • SNV Effect Predictions:
      • Position Specific and Run of Homozygosity:
    • Gene Filters
  • Variant Dashboard
    • Study Toolbar
    • Analysis and Query Tabs
    • Variant Table Toolbar
    • External Links and Databases
    • Results Table
      • Case Analysis
        • SNV and InDels Table
        • CNV and SV Table
      • Cohort Analysis and Search Across All Experiments
        • Participant by participant
        • Gene by gene
  • IGV browser
  • Label and Tag a variant
    • Labeling
    • Tagging
      • Listing all tags for a variant
  • Save, share and delete a study
  • CNV/SV analysis
    • Workflow CNAG portal GPAP
    • Workflow RD-Connect GPAP
    • Variant calling tools
    • Annotation
    • Data quality
    • ClinVar
    • Internal Frequency
  • Patient Matchmaking
  • Clinical Report