VarSeq Manual

Version 2.2.3 (Previous versions)

Copyright © 2000-2021 Golden Helix, Inc.

The VarSeq® software streamlines the process of annotating and filtering variants obtained from next generation sequencing pipelines, allowing both research scientists and clinicians to find variants of interest in a very efficient and straightforward manner. VarSeq simplifies the user interface and provides a scalable architecture featuring repeatable workflows, note taking and reporting, and filter parameter prototyping.

Acknowledgments

VarSeq would not exist without the generous contributions of many people. We would particularly like to thank all of the VarSeq alpha testers and everyone who has given VarSeq a try and provided feedback.

Trademarks Used

VarSeq is a registered trademark of Golden Helix. Affymetrix, GeneChip and the Affymetrix logo are registered trademarks used by Affymetrix, Inc. Microsoft, Microsoft SQL, Transact-JQL, Excel, Access and ODBC are registered trademarks of Microsoft, Inc. Stat/Transfer is a registered trademark of Circle Systems, Inc. Oracle, Oracle PL-SQL and SQL Server are registered trademarks of Oracle, Inc. IBM and DB2 are registered trademarks of IBM. SAS is a registered trademark of SAS, Inc. Sybase is a registered trademark of Sybase,Inc. Any other incidentally used names that are registered trademarks are trademarks of their respective owners.

• Installing and Initializing
  • Installation Under Windows
  • Installation Under Ubuntu or Compatible Distributions
  • Installation Under RHEL7 and CentOS7 Linux Distributions
  • Linux Configuration in a Shared Environment
  • Installation Under Mac OS X
  • Setting System Defaults with hosts.json File
• Release Notes
  • 2.2.3
  • 2.2.2
  • 2.2.1
  • 2.2.0
  • 2.1.1
  • 2.1.0
  • 2.0.2
  • 2.0.1
  • 1.5.0
  • 1.4.7
  • 1.4.6
  • 1.4.5
  • 1.4.4
  • 1.4.3
  • 1.4.2
  • 1.4.1
  • 1.4.0
  • 1.3.6
  • 1.3.5
  • 1.3.4
  • 1.3.3
  • 1.3.2
  • 1.3.1
  • 1.3.0
  • 1.2.2
  • 1.2.1
  • 1.2.0
  • 1.1.4
  • 1.1.3
  • 1.1.2
  • 1.1.1
  • 1.1.0
  • 1.0.4
  • 1.0.3
  • 1.0.2
  • 1.0.1
  • 1.0.0
• Launching VarSeq
  • Login and Register Dialog
  • VarSeq Viewer
  • Adjusting Proxy Settings
  • Create a New Project
• Frequently Asked Questions
  • How can I filter my variants using a list of gene names?
  • How can I compute coverage statistics for my sample BAM files?
  • How can I prioritize my variants based on a known phenotype?
• Navigating VarSeq
  • VarSeq Views
  • VarSeq Menus
  • VarSeq Tool Bar
  • Saving a Project as a Template
  • View Menus
• Importing Variants
  • Select Files to Import
  • Select Relationship
  • Edit Sample Information
  • Modify How Fields in the Variant Files are Imported
  • Import Summary
• Exporting Data from VarSeq
  • Export to Text
  • Export to VCF
  • Export to Excel (XLSX)
• Filter View
  • Lock the Filter Chain
  • Edit Titles
  • Update Current Table View to Filter Results
  • Disable or Enable Filter
  • Invert Filter Logic
  • Configure Filter Chain or Container
  • Configure Filter Card
  • Add Filter
  • Add Filter Container
  • Delete
  • Error or Status Messages
• Table View
  • General Table Actions
  • Icons on the Tool Bar for a Table
  • Table Filters
  • Searching the Table
  • Record Sets
  • Detail View
• GenomeBrowse View
  • Navigating the GenomeBrowse Window
  • Saving Plots from a GenomeBrowse Window
• Note View
  • Creating a New Note
  • Opening an Existing Note
  • Editing a Note
• Report View
  • Adding a New Template
  • Creating a Report
  • Adding Variants to the Report
  • Customizing Reports
  • Reports Hosted on VSWarehouse Server
• VSClinical
  • ACMG Guidelines
  • AMP Guidelines
  • References
• Customizing VSClinical Reports
  • The Inputs: Variants, Sample and Results
  • The Outputs
  • Customizing Templates
  • System Filter Functions Reference
• Assessment Catalog View
  • Creating a New Assessment Catalog
  • Editing Assessment Catalog Schemas
  • Record Entry
  • Batch Assessment Import
  • Annotation Using the Assessment Catalog
  • Local Assessment Export
  • Assessment Catalogs Hosted on VSWarehouse Server
• Log View
• Web Browser
• VarSeq Algorithms
  • Genotype Zygosity
  • Frequency Aware Zygosity
  • GT Style Genotype
  • Compute Fields
  • Mendel Error
  • Variant Type
  • Count Alleles
  • Annotate Transcripts
  • Annotate Overlapping CNVs
  • Annotate Overlapping Genes
  • Annotate Overlapping Regions
  • Annotate Regions
  • Aggregate Compute Fields
  • Sample PhoRank Gene Ranking
  • Count Alleles By Gene
  • Match Gene List (Per Sample)
  • Compound Het Detection
  • Variant PhoRank Gene Ranking
  • Aggregate Filtered Variants
  • Match Genes Linked to Phenotypes
  • Match Gene List
  • Targeted Region Coverage
  • Binned Region Coverage
  • Sample Statistics
  • CNV Caller on Binned Regions
  • CNV Caller on Target Regions
  • LoH Caller
  • Importing Regions and CNVs
  • Select Files to Import
  • Setting the Parsing Parameters for Text Input
  • Associating Inputs with Existing Samples
  • Setting the Import Field Behavior
  • Import Summary
  • Annotate Variants Matching Current Sample
  • Annotate Regions Matching Current Sample
  • Annotate CNVs Matching Current Sample
  • Latest Sample Assessment
  • Latest Sample Assessment
• Expression Editor
  • Expression Inputs
  • Example Expressions
• GenomeBrowse Options for Specific Plot Types
  • Numeric Value Plot
  • Variant Maps
  • Linkage Disequilibrium
  • Heat Maps
  • BAM File Type
  • BED File Type
  • Cytoband Sources
  • Interval Sources
  • Gene Sources
  • Read Alignment Sources
  • Allele Sequence Sources
  • Variant Sites
  • General Control Panels
• The Data Source Library
  • Navigating the Data Source Library
  • Data Source Types Available through the Data Source Library
  • The Data Source Library as an Plot Dialog
  • Downloading Data
  • Exporting Data
  • Source Information Editor
• Genome Assemblies
  • Bundled Genome Assemblies
  • Switching Genome Assemblies
  • Managing Genome Assembly Views
• Annotation Convert Source Wizard
  • Opening the Convert Source Wizard
  • Convert a 2Bit File
  • Converting a FASTA File
  • Converting a VCF File
  • Converting a BED File
  • Converting a GTF File
  • Converting a WIG (Fixed or Variable Step) File
  • Converting a Delimited Text File
  • Converting an IDF or TSF File
  • Select a Genome Assembly
  • Documentation Step
  • Confirmation of the Specified Parameters
  • Converting Data Sources to Annotation Source
• Evernote: Cloud-based Project Documentation
  • Linking to an Evernote Account
  • Creating a New Note
  • Opening an Existing Note
  • Editing a Note
• OMIM
• CADD
  • Estimating CADD Scores
• MedGenome OncoMD
• VarSeq Pipeline Runner
  • Launching VSPipeline on Windows Operating Systems
  • Launching VSPipeline on Linux and RHEL Operating Systems
  • Launching VSPipeline on MacOS X
  • Downloading Annotations
  • VSPipeline Command Line Arguments
  • Accessing Help for Commands
  • Command Specification Tips
  • Waiting For Task Completion
  • Deploying VSPipeline to a Production Environment
  • A Note on Users and Logged In State
  • Retrieving and Logging in with a Temporary License Token
  • Example Workflow
  • IDs Used in Table Exports
• VarSeq CNV Command Line Runner
  • Command Line Arguments
  • Command Specification Tips
  • Gene Panel Workflow
  • Exome Workflow
  • Whole Genome Workflow
• VarSeq CNV Reference Manager
  • Reference Location
  • Exploring Current Reference Folder
  • Adding Reference Samples
• Filtered Targets Wizard
  • Add Reference Set Files
  • Set Target Region Filters
  • Confirm Target Track Options
• VSWarehouse Client-Side Integration
  • Connecting to a VSWarehouse Server
  • Managing and Using Warehouse Projects
  • Using Warehouse Variants Annotation Sources
  • Warehouse Hosted Reports
  • Warehouse Hosted Assessment Catalogs
• Customizing Reports
  • The Layout
  • The Render Function
  • Example: Adding a Data Field to a Report
  • Example: Selecting a Variant Transcript
• EULA
• Appendix
  • Getting Started Guides
• References