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• Collapsing (Old)
• Fisher's Exact Test
• Function Options
  • Annotation Level Filter Options
  • Cohort Level Filter Options
  • Genotype Level Filter Options
  • Variant Level Filter Options
• Generate Ped Map
  • FlashPCA
• List Trio Compound Het
• List Trio Denovo
• List Variant Genotype
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  • Coverage Summary
  • Definitions
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    • 1000 Genomes
    • CCR
    • DenovoDB
    • DiscovEHR
    • EVS
    • ExAC
    • General dbGaP Information
      • DbGaP downloads
        • EVS individual data
      • DbGaP uploads
    • Gerp
    • GnomAD
    • Kaviar
    • KnownVar
    • LIMBR
    • MGI
    • MTR
    • PrimateAI
    • REVEL
    • RVIS
    • SubRVIS
    • Swedish schizophrenia controls
    • TraP
    • Wellderly
  • Family Analysis
  • Functions
    • Cohort Analysis Functions
      • Collapsing Lite
      • List Parental Mosaic
      • List Parent Comp Het
      • List Sibling Comp Het
      • List Trio
      • List Variant
      • List Variant Genotype Lite
      • List VCF
      • Logistic Regression
    • Collapsing
    • Collapsing Compound Het
    • Coverage Analysis Functions
      • Site Coverage Comparison
    • Coverage Comparison
    • External Datasets Functions
      • List 1000 Genomes
      • List CCR
      • List Denovo DB
      • List Gerp
      • List gnomAD Exome
      • List gnomAD Genome
      • List Kaviar
      • List MGI
      • List PrimateAI
      • List REVEL
      • List Rvis
      • List subRVIS
      • List Trap
    • Linear Regression
    • List EVS
    • List ExAC
    • List Flanking Sequence
    • List Gene Dx
    • List Known Var
    • List Variant Annotation
    • Non Database functions
      • PPI
    • Site Coverage Summary
    • Variant Annotation Functions
  • Internal Toolkit
    • Cohort Selection
    • Diagnostic Analysis Framework
      • Analysis Commands
        • Recommended ATAV Commands
          • Coverage ATAV Command
          • Non-Trio Report ATAV Command
          • Trio Report ATAV Commands
        • Recommended generateNonTrioVariantReport Command
        • Recommended generateVariantReport Command
          • Filtering Rules
            • Non-Trio Rules
            • Summary Table Rules
            • Tier 1 Rules
            • Tier 2 Rules
    • Kinship Pruning
    • SNV Data Sets
  • Output Columns
    • Annotation Level Columns
    • Cohort Level Columns
    • Genotype Level Columns
    • Variant Level Columns
  • Publications
  • Quick Start
  • SAGA
    • SAGA Sample Ingest
  • SGE Cluster Guide
  • Tester's Guide

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