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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

10.2 Preparing Log2 Ratio Data

The CNAM optimal segmenting algorithm uses log2 ratio data as input. Therefore, before you can begin copy number analysis, you must import log2 data into an SVS project.

For the Affymetrix 500k, SNP 5.0, and SNP 6.0 arrays, CNAM supports reading CEL intensity files and calculating normalized log2 ratios for copy number segmentation and analysis in SVS. For details about reading CEL intensity files, see Affymetrix Files.

For the Affymetrix 10k, 100k, and 500k arrays, you may use the Affymetrix CNAT Batch Analysis tool to create CNT files; or for the 100k, 500k, and SNP 6.0 arrays use Genotyping Console to create CNCHP files. These files contain normalized log2 ratios and can be imported into SVS for analysis in CNAM. See Affymetrix Files for instructions on creating and importing these files. Once the files have been parsed to extract the log2 ratio values, the data is ready for copy number analysis.

For the Illumina platform, you must use GenomeStudio with the SVS DSF Export Plug-In to export the log2 ratio values from your GenomeStudio project. For instructions on how to install and use the plug-in, see Exporting Data from GenomeStudio.

For the Agilent platform, you must use the Agilent import menu item and select the correct intensity field for importing the log2 ratio data. See Agilent Files for more information.

For the NimbleGen platform, you must use the NimbleGen Data Summary Files import menu item and select at least one field to import. See NimbleGen Data Summary Files for more information.

You may also create a minimal data file with your own normalized log2 ratio data using the Affymetrix CNT file format. This file must contain log2 ratio data and marker map data. See Affymetrix CNT File Format for details. You can then import the Affymetrix CNT files to create a spreadsheet of log2 ratio data.

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