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VarSeq v2.3.0 Instructions for Use
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VarSeq Suite

  • 1. VarSeq Suite Device Information
  • 2. Introduction to the VarSeq Suite
  • 3. Installing and Initializing
  • 4. Operating Instructions
    • 4.1. Launching VarSeq
    • 4.2. Navigating VarSeq
    • 4.3. VarSeq Projects
    • 4.4. Importing Variants
    • 4.5. VarSeq Views
      • 4.5.1. Filter View
      • 4.5.2. Table View
      • 4.5.3. GenomeBrowse View
      • 4.5.4. Note View
      • 4.5.5. VSReport View
      • 4.5.6. VSReports Templates
      • 4.5.7. VSClinical
      • 4.5.8. Assessment Catalog View
      • 4.5.9. Log View
      • 4.5.10. Web Browser
    • 4.6. Copy Number Analysis
      • 4.6.1. VarSeq CNV Caller
      • 4.6.2. VarSeq CNV Command Line Runner
      • 4.6.3. VarSeq CNV Reference Manager
      • 4.6.4. Filtered Targets Wizard
    • 4.7. Annotations
      • 4.7.1. The Data Source Library
      • 4.7.2. Expression Editor
      • 4.7.3. GenomeBrowse Options for Specific Plot Types
      • 4.7.4. Genome Assemblies
      • 4.7.5. Annotation Convert Wizard
      • 4.7.6. OMIM
      • 4.7.7. CADD
      • 4.7.8. gautil Documentation
    • 4.8. Variant Algorithms
      • 4.8.1. Genotype Zygosity
      • 4.8.2. Frequency Aware Zygosity
      • 4.8.3. GT Style Genotype
      • 4.8.4. Compute Fields
      • 4.8.5. Mendel Error
      • 4.8.6. Variant Type
      • 4.8.7. Count Alleles
      • 4.8.8. Annotate Transcripts
      • 4.8.9. Annotate Regions
      • 4.8.10. Aggregate Compute Fields
      • 4.8.11. Sample PhoRank Gene Ranking
      • 4.8.12. Count Alleles By Gene
      • 4.8.13. Match Gene List (Per Sample)
      • 4.8.14. Compound Het Detection
      • 4.8.15. Variant PhoRank Gene Ranking
      • 4.8.16. Aggregate Filtered Variants
      • 4.8.17. Match Genes Linked to Disorders
      • 4.8.18. Match Genes Linked to Phenotypes
      • 4.8.19. Match Panels (Per Sample)
      • 4.8.20. Match String List
      • 4.8.21. Annotate Variants Matching Current Sample
      • 4.8.22. Annotate Regions Matching Current Sample
      • 4.8.23. Latest Sample Assessment
      • 4.8.24. Sample ACMG Classifier
      • 4.8.25. Gene List Coverage Statistics
      • 4.8.26. Variant Site ACMG Classifier
    • 4.9. CNV Algorithms
      • 4.9.1. CNV Caller on Target Regions
      • 4.9.2. LoH Caller
      • 4.9.3. CNV Caller on Binned Regions
      • 4.9.4. Annotate Overlapping CNVs
      • 4.9.5. Annotate Overlapping Genes
      • 4.9.6. Annotate Overlapping Regions
      • 4.9.7. ACMG CNV Site Classifier
      • 4.9.8. CNV PhoRank Gene Ranking
      • 4.9.9. Copy Number Probability/Segregation
      • 4.9.10. ACMG CNV Site Classifier
      • 4.9.11. Latest CNV Sample Assessments
      • 4.9.12. Annotate Overlapping CNVs Matching Current Sample
    • 4.10. Other Algorithms
      • 4.10.1. Targeted Region Coverage
      • 4.10.2. Binned Region Coverage
      • 4.10.3. Sample Statistics
      • 4.10.4. Annotate Fusions
      • 4.10.5. Annotate Overlapping Genes
      • 4.10.6. Annotate Rearrangements Against Overlapping Regions
      • 4.10.7. Importing Regions and CNVs
      • 4.10.8. Importing Breakends
    • 4.11. VSWarehouse
    • 4.12. VarSeq Pipeline Runner
    • 4.13. Frequently Asked Questions
    • 4.14. Exporting Data from VarSeq
  • 5. EULA
  • 6. Trouble Shooting Errors

References

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

VarSeq Suite Instructions For Use¶

Version 2.3.0 (Previous versions)

Copyright © 2014 -2022 Golden Helix, Inc.

VarSeq Suite

  • 1. VarSeq Suite Device Information
  • 2. Introduction to the VarSeq Suite
  • 3. Installing and Initializing
  • 4. Operating Instructions
  • 5. EULA
  • 6. Trouble Shooting Errors

References

  • WebSite for VarSeq
  • Golden Helix Blog
  • Tutorials & Resources
  • Release Notes
  • Known Issues
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1. VarSeq Suite Device Information
Copyright © 2022, Golden Helix