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SVS7 Manual

Installing and Initializing
- Installation Overview
- Release Notes
Understanding the Interface and Workflow
- General Genetic Association Analysis Workflow
- Interface Overview
- Navigating the Welcome Screen
- Project Navigator
Importing Your Data Into A Project
- Importing Data
- Text File
- Third Party File
- PED/TPED/BED File
- Golden Helix, Inc. DSF File
- Legacy Golden Helix, Inc. GHD File
- Public Data
- Affymetrix Files
- Illumina
- Agilent Files
- NimbleGen Data Summary Files
- Importing PBAT Family-Based Data
- HapMap
- VCF
- Mach Output
- Parallele Long File
Genetic Marker Maps and Affymetrix Library Files
- Genetic Marker Maps Overview
- Convert Text File into Marker Map DSM Format
- Download from Golden Helix, Inc.
- Download Affymetrix Annotation Files
- Managing the MarkerMaps Folder
- Applying a Genetic Marker Map to a Spreadsheet
- Exporting an Applied Genetic Marker Map to a DSM file
- Downloading Affymetrix Library (CDF) Files
Spreadsheets
- Spreadsheet Overview
- Working with a Single Spreadsheet
- Editing a Spreadsheet
- Working with Multiple Spreadsheets
Scripting and Other Integrated Statistical Tools
- Integrated Tools Overview
- The Python Shell Window
- The Python Editor Window
- Running Scripts
- Obtaining Add-On Scripts
- Scripting Reference
Data Quality Assessment
- Quality Assurance Overview
- Quality Assurance Procedures
- Genotype Statistics by Marker
- Genotype Filtering by Marker
- Genotype Statistics by Sample
- PBAT Family-Based QC Statistics
- Principal Component Analysis Overview
- Genotypic Principal Component Analysis
- Numeric Principal Component Analysis
- Correcting for Stratification by Genomic Control
- Identity by Descent Estimation
- Inbreeding Coefficients
- LD Pruning
- Wave Detection and Correction
Analysis
- Genotype Association Tests
- Haplotype Association Tests
- Haplotype Block Detection
- Runs of Homozygosity
- Numeric Association Tests
- Regression Analysis
- Fisher’s Exact Test for Binary Predictors
PBAT Family-Based Analysis
- PBAT Family-Based Analysis Overview
- Using PBAT Capabilities Through SVS
- Pre-Study Power Calculation
- PBAT Genotype Analysis
- PBAT CNV Analysis
Copy Number Analysis
- Copy Number Analysis Overview
- Preparing Log2 Ratio Data
- Using CNAM Optimal Segmenting
- Outputs from CNAM Optimal Segmenting
- Manipulating and Analyzing CNAM Output
- CNV Association Tests
- Visualizing Copy Number Analysis Results
Sequence Analysis
- Sequence Analysis Overview
- Preparing Genotypes for Sequence Analysis
- Filtering with Annotation Tracks
- Collapsing Methods
- Sequence Analysis Tutorial
Visualizing Data
- Types of Plots Available
- Plot Viewer
- Genome Browser
- Opening the Plot Viewer
- Using the Graph Control Interface
- Using the Data Console
- Docking, Un-docking or Hiding Plot Viewer Subwindows
- Zooming in the Graph View
- Using LD Plots
- Haplotype Tables
- Heat Maps
- Creating Specialized Plots
Genome Browser
- Genome Maps
- Creating Genome Maps
- Switching Genome Maps
- Network Annotation Tracks
- Local Annotation Tracks
- Annotation Track Manager
Export Options for Data and Plots
- Exporting Spreadsheet Data
- Saving or Printing Graphs
Formulas and Theories: The Science Behind SNP and Variation Suite
- General Statistics
- Permutation Testing Methodology
- Linear Regression
- Logistic Regression
- Haplotype Frequency Estimation Methods
- Formulas for Principal Component Analysis
- Runs Of Homozygosity (ROH) Algorithm
- Quantile Normalization of Affymetrix CEL Files
- CNAM Optimal Segmentation Algorithm
Appendices
EULA
Installing the Third-Party Condor ®
- Installing Condor ® Overview
- Downloading and Using the Installation Wizard
- Troubleshooting Techniques and Common Issues
Extracting Affymetrix Copy Number Data for use in SVS
- Extracting Affymetrix Copy Number Data Overview
- Creating CNT Files using the Affymetrix CNAT Batch Analysis Tool
- Creating CNCHP Files Using Affymetrix Genotyping Console 2.0
- Affymetrix CNT File Format
Exporting Data from GenomeStudio
- Exporting Data From GenomeStudio Overview
- Exporting Genotype Data using the Final Report
- Exporting Data using the SVS DSF Export 4.0 Plug-In
Platform Notes
- Microsoft Windows
Hardware Acceleration
- Using Hardware Acceleration
A Glossary of Terms Used in Genetic Analysis
References

6.1 Integrated Tools Overview

A common trade-off faced by program and tool developers is providing the convenience of a Graphical User Interface (GUI) with the raw power and automation of command line oriented programs. Often, flexibility of tool use and data manipulation is sacrificed for informative visual displays and interactive dialogs. Golden Helix, Inc., Inc. has developed a unique solution to not only take advantage of these two paradigms but also open the way for cross-communication between other tools used in data analysis. By providing full access to SVS’s features through the powerful Python scripting language, this program provides functionality and support for collaboratively developing new analysis techniques.

Key features of this tool are:

A Python script editor to edit and write new scripts from within the SVS program.
A Python shell window where users can develop new techniques while running the program in GUI mode.
By using Python as SVS’s scripting language, your scripts have access to the more powerful constructs of a complete programming language.
New analysis techniques can be dynamically added to your private scripts menu or they can be published on a shared network drive for others to use.
GUI dialogs to collect important parameters can be dynamically created as part of a script.
The ability to add data and results from many tools to the project navigator window.
Scripts can be run from the command line without starting SVS by executing the program with the
SVS --script=<script name>.py [optional script args] command.

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