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• Welcome to Biomedical Genomics Workbench
  • Introduction to Biomedical Genomics Workbench
  • Available documentation
  • The material covered by this manual
  • We welcome your comments and suggestions
  • Contact information
    • Contact for the Biomedical Genomics Workbench
    • New program feature request
    • Getting help
• Introduction to user interface, workflows, and tracks
  • The start screen
    • The getting started table
    • Import of example data
  • The user interface
    • The Toolbox
  • Workflows - an overview
  • The track format
    • Track types
    • The Genome Browser
• Ready-to-Use Workflows descriptions and guidelines
  • General Workflow
  • Somatic Cancer
  • Hereditary Disease
• Getting started
  • Reference data
    • The Workbench Reference data location
    • Space requirements
    • Where reference data is downloaded from
    • Download and configure reference data
    • Create a custom Reference Data Set
    • Exporting reference data for use in external applications
    • Troubleshooting reference data downloads
  • Create new folder
  • Import sequencing data
    • How to import data
  • Prepare sequencing data
    • Import adapter trim list
    • How to run the Prepare Overlapping Raw Data ready-to-use workflow
    • How to run the Prepare Raw Data ready-to-use workflow
    • Output from the Prepare Overlapping Raw Data and Prepare Raw Data workflows
    • How to check the output reports
• Whole genome sequencing (WGS)
  • General Workflows (WGS)
    • Annotate Variants (WGS)
    • Identify Known Variants in One Sample (WGS)
  • Somatic Cancer (WGS)
    • Filter Somatic Variants (WGS)
    • Identify Somatic Variants from Tumor Normal Pair (WGS)
    • Identify Variants (WGS)
  • Hereditary Disease (WGS)
    • Filter Causal Variants (WGS-HD)
    • Identify Causal Inherited Variants in Family of Four (WGS)
    • Identify Causal Inherited Variants in Trio (WGS)
    • Identify Rare Disease Causing Mutations in Family of Four (WGS)
    • Identify Rare Disease Causing Mutations in Trio (WGS)
    • Identify Variants (WGS-HD)
• Whole exome sequencing (WES)
  • General Workflows (WES)
    • Annotate Variants (WES)
    • Identify Known Variants in One Sample (WES)
  • Somatic Cancer (WES)
    • Filter Somatic Variants (WES)
    • Identify Somatic Variants from Tumor Normal Pair (WES)
    • Identify Variants (WES)
    • Identify and Annotate Variants (WES)
  • Hereditary Disease (WES)
    • Filter Causal Variants (WES-HD)
    • Identify Causal Inherited Variants in Family of Four (WES)
    • Identify Causal Inherited Variants in Trio (WES)
    • Identify Rare Disease Causing Mutations in Family of Four (WES)
    • Identify Rare Disease Causing Mutations in Trio (WES)
    • Identify Variants (WES-HD)
    • Identify and Annotate Variants (WES-HD)
• Targeted amplicon sequencing (TAS)
  • General Workflows (TAS)
    • Annotate Variants (TAS)
    • Identify Known Variants in One Sample (TAS)
  • Somatic Cancer (TAS)
    • Filter Somatic Variants (TAS)
    • Identify Somatic Variants from Tumor Normal Pair (TAS)
    • Identify Variants (TAS)
    • Identify and Annotate Variants (TAS)
  • Hereditary Disease (TAS)
    • Filter Causal Variants (TAS-HD)
    • Identify Causal Inherited Variants in Family of Four (TAS)
    • Identify Causal Inherited Variants in Trio (TAS)
    • Identify Rare Disease Causing Mutations in Family of Four (TAS)
    • Identify Rare Disease Causing Mutations in Trio (TAS)
    • Identify Variants (TAS-HD)
    • Identify and Annotate Variants (TAS-HD)
• Whole Transcriptome Sequencing (WTS)
  • Analysis of multiple samples
  • Annotate Variants (WTS)
  • Compare variants in DNA and RNA
  • Identify Candidate Variants and Genes from Tumor Normal Pair
  • Identify variants and add expression values
  • Identify and Annotate Differentially Expressed Genes and Pathways
• How to edit application workflows
  • Introduction to customized data analysis
  • How to edit preinstalled workflows
• Plugins
• Appendix
  • Reference data overview
  • Mini dictionary
• Bibliography

The material covered by this manual

This usermanual provides introductory material on how to work with the software, including the import and initial handling of data and a guide to the data types and user interface. Its main focus is to provide guidance on how to use the workflows that come with the software.

Also included is an appendix where there is a table listing the available reference data as well as a small dictionary of terminology used in the Biomedical Genomics Workbench. The dictionary is not exhaustive, but we hope it will serve as a useful reference, especially for new users.

For comprehensive descriptions of the features and functionalities of the individual tools, please refer to the Biomedical Genomics Workbench reference manual.

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