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VarSeq v2.2.5 Instructions for Use
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VarSeq Suite

  • 1. VarSeq Suite Device Information
  • 2. Installing and Initializing
  • 3. Operating Instructions
    • 3.1. Launching VarSeq
    • 3.2. Frequently Asked Questions
    • 3.3. Navigating VarSeq
    • 3.4. Importing Variants
    • 3.5. Exporting Data from VarSeq
    • 3.6. VarSeq Views
      • 3.6.1. Filter View
      • 3.6.2. Table View
      • 3.6.3. GenomeBrowse View
      • 3.6.4. Note View
      • 3.6.5. VSReport View
      • 3.6.6. VSReports Templates
      • 3.6.7. VSClinical
      • 3.6.8. Assessment Catalog View
      • 3.6.9. Log View
      • 3.6.10. Web Browser
    • 3.7. Clinical Interpretation
      • 3.7.1. VSClinical ACMG
      • 3.7.2. VSClinical AMP
      • 3.7.3. Project Options
      • 3.7.4. Customizing VSClinical Reports
      • 3.7.5. Manage Gene List Dialog
      • 3.7.6. Gene and Transcript Preferences
    • 3.8. Copy Number Analysis
      • 3.8.1. VarSeq CNV Caller
      • 3.8.2. VarSeq CNV Command Line Runner
      • 3.8.3. VarSeq CNV Reference Manager
      • 3.8.4. Filtered Targets Wizard
    • 3.9. Annotations
      • 3.9.1. The Data Source Library
      • 3.9.2. Expression Editor
      • 3.9.3. GenomeBrowse Options for Specific Plot Types
      • 3.9.4. Genome Assemblies
      • 3.9.5. Annotation Convert Wizard
      • 3.9.6. OMIM
      • 3.9.7. CADD
      • 3.9.8. gautil Documentation
    • 3.10. Variant Algorithms
      • 3.10.1. Genotype Zygosity
      • 3.10.2. Frequency Aware Zygosity
      • 3.10.3. GT Style Genotype
      • 3.10.4. Compute Fields
      • 3.10.5. Mendel Error
      • 3.10.6. Variant Type
      • 3.10.7. Count Alleles
      • 3.10.8. Annotate Transcripts
      • 3.10.9. Annotate Regions
      • 3.10.10. Aggregate Compute Fields
      • 3.10.11. Sample PhoRank Gene Ranking
      • 3.10.12. Count Alleles By Gene
      • 3.10.13. Match Gene List (Per Sample)
      • 3.10.14. Compound Het Detection
      • 3.10.15. Variant PhoRank Gene Ranking
      • 3.10.16. Aggregate Filtered Variants
      • 3.10.17. Match Genes Linked to Disorders
      • 3.10.18. Match Genes Linked to Phenotypes
      • 3.10.19. Match Panels (Per Sample)
      • 3.10.20. Match String List
      • 3.10.21. Annotate Variants Matching Current Sample
      • 3.10.22. Annotate Regions Matching Current Sample
      • 3.10.23. Latest Sample Assessment
      • 3.10.24. Sample ACMG Classifier
      • 3.10.25. Gene List Coverage Statistics
      • 3.10.26. Variant Site ACMG Classifier
    • 3.11. CNV Algorithms
      • 3.11.1. CNV Caller on Target Regions
      • 3.11.2. LoH Caller
      • 3.11.3. CNV Caller on Binned Regions
      • 3.11.4. Annotate Overlapping CNVs
      • 3.11.5. Annotate Overlapping Genes
      • 3.11.6. Annotate Overlapping Regions
      • 3.11.7. Sample ACMG CNV Classifier
      • 3.11.8. CNV PhoRank Gene Ranking
      • 3.11.9. Copy Number Probability/Segregation
      • 3.11.10. ACMG CNV Site Classifier
      • 3.11.11. Latest Sample CNV Assessment
      • 3.11.12. Annotate CNVs Matching Current Sample
    • 3.12. Other Algorithms
      • 3.12.1. Targeted Region Coverage
      • 3.12.2. Binned Region Coverage
      • 3.12.3. Sample Statistics
      • 3.12.4. Annotate Fusions
      • 3.12.5. Annotate Overlapping Genes
      • 3.12.6. Importing Regions and CNVs
      • 3.12.7. Importing Breakends
    • 3.13. VSWarehouse
    • 3.14. VarSeq Pipeline Runner
  • 4. EULA
  • 5. Trouble Shooting Errors

References

  • WebSite for VarSeq
  • Golden Helix Blog
  • Tutorials & Resources
  • Release Notes
  • Known Issues

3.12. Other AlgorithmsΒΆ

Other Algorithms

  • 3.12.1. Targeted Region Coverage
  • 3.12.2. Binned Region Coverage
  • 3.12.3. Sample Statistics
  • 3.12.4. Annotate Fusions
  • 3.12.5. Annotate Overlapping Genes
  • 3.12.6. Importing Regions and CNVs
  • 3.12.7. Importing Breakends
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3.12.1. Targeted Region Coverage
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3.11.12. Annotate CNVs Matching Current Sample
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