Beginner

Genome-Wide SNP Association Tutorial

Created August 3, 2010
The following short tutorial covers an abbreviated SNP analysis workflow on a whole-genome scale.

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Beginner

Importing and Merging Data in SVS 7

Updated June 9, 2010
This tutorial introduces how to import and merge data including pedigree data, phentype data, and genetic data.

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SNP Analysis

Updated November 6, 2009
The following tutorial covers an entire SNP analysis workflow on a whole-genome scale. It is designed to systematically introduce you to a few of the new features and enhancements in SVS 7.

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Intermediate

Comparing Copy Number Variations Between Tumors and Normals Using the Affymetrix MIP Array

Updated June 18, 2010
This tutorial leads you through analyzing MIP (Molecular Inversion Probe) copy number data, as provided by Affymetrix, to detect differences between 17 normal and 25 tumor samples. Though this tutorial applies specifically to Affymetrix MIP data, the concepts can be applied to any copy number project where two or more sets of samples are being compared.

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Copy Number Variation (CNV) Analysis

Updated March 8, 2010
This tutorial covers an entire CNV analysis workflow in SVS 7 focusing on methods for processing raw intensity data, performing quality assurance, identifying regions of copy number variation (CNV), visualizing copy number data, and performing association analysis on a variety of copy number covariates.

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Family-Based Analysis

November 17, 2009
This tutorial leads you through family-based association analysis using the PBAT statistical package incorporated into SNP & Variation Suite 7. Covered workflows include data preparation, quality assurance testing, association analysis, and basic visualization of results.

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LD and Haplotype Analysis

Updated March 8, 2010
This tutorial leads you through various LD and haplotype analyses in SVS 7. For demonstration purposes, a simulated dataset is used consisting of actual Affymetrix 500K genotypes from the four HapMap populations (Phase II) and a fake case/control status.

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Runs of Homozygosity Analysis

Updated July 2010
Runs of Homozygosity (ROH) analysis is a novel analytic approach that first identifies patterned clusters of SNPs demonstrating extended homozygosity and then employs both genome-wide and regionally-specific statistical tests for association to disease. Using a simulated dataset, this tutorial will lead you step-by-step through the workflow for finding ROHs outlined in Dr.Todd Lencz's paper.

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Advanced

Recalling Genotypes with BEAGLECALL

August 27, 2010
This tutorial focuses on BEAGLECALL showcasing add-on scripts required for importing and exporting back and forth between SVS to BEAGLECALL. It also provides a workflow to maximize the efficiency of these products. Many of the scripts featured in this tutorial can also be used with BEAGLE, which has the same file formats as BEAGLECALL.

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CNV PCA Search

November 12, 2009
This tutorial leads you through a holistic approach for determining the optimal number of principal components to correct CNV data for batch effects and other stratification issues with principal component analysis.

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Creating a Genome Map in SVS 7

August 9, 2010
Currently there are several available genome maps within SVS 7, including the human, cattle and soybean genomes. But what if you are studying corn and you find that there is no genome map available for the species Zea Mays (maize or corn)? Well if you have the necessary information available or you are willing to locate it independently, you will find that it is simple and straightforward to create your own genome map in SVS.

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