Manuals
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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
Somatic Cancer (TAS)
Subsections
Filter Somatic Variants (TAS)
Identify Somatic Variants from Tumor Normal Pair (TAS)
Identify Variants (TAS)
Identify and Annotate Variants (TAS)
