QUICK LINKS
SNP & Variation Suite
GenomeBrowse
Robert Kleta and His Newly-Formed Team Publish in a Few Short Months with SVS
Fundamentals |
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Getting Started with SVSThis video tutorial introduces you to the SVS interface and methodically takes you through starting your own project including exploring drop-down menus, and plotting association results. Access the Video Tutorial » | Runtime: 20 minutes |
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Introduction to SVS 7: Importing, combining datasets, spreadsheet manipulation, and filteringThis tutorial seeks to guide you through basic importing and spreadsheet manipulation. The steps outlined aim to make you a power user by providing examples of functions that are often under-utilized but can make spreadsheet manipulation a breeze. |
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SNP Genome-Wide AssociationThe following tutorial is designed to systematically introduce you to a number of techniques for genome-wide association studies. It is not meant to replicate all the workflows you might use in a complete analysis, but instead touch on a sampling of the more typical scenarios you may come across in your own studies. |
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VIDEO: Genome-Wide SNP AssociationThe following short tutorial covers an abbreviated SNP analysis workflow on a whole-genome scale. Access the Video Tutorial » | Runtime: 9 minutes |
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Intermediate |
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Comparing Copy Number Variations Between Tumors and Normals Using the Affymetrix MIP ArrayThis 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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Introduction to DNA-SeqThis tutorial covers the introductory steps and procedures that will prepare your dataset for further NGS analysis and filtering. The steps include data import, annotation track download and filtering, and variant classficiation. |
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LD and Haplotype AnalysisThis 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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Quantitative Haplotype Association and Haplotype Trend RegressionThis tutorial provides a step-by-step workflow for generating haplotype frequency tables from and LD plot of your genotype data and then using those tables to perform numerical association or regression. |
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VIDEO: Quantitative Haplotype Association and Haplotype Trend RegressionThis tutorial provides a step-by-step workflow for creating an LD plot from a marker mapped spreadsheet, defining a haplotype block for a region of interest, and generating haplotype frequency tables for that block. Access the Video Tutorial » | Runtime:2:35 |
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Regression with CovariatesThis tutorial provides an in-depth look at the regression capabilities in SVS. It will cover controlling for confounding variables, model comparison, and stepwise regression. The genotype spreadsheet included in the project file contains PCA-corrected numeric SNP columns for an additive model. The phenotype information is simulated. |
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Runs of Homozygosity AnalysisUsing a simulated dataset, this tutorial will lead you step-by-step through the workflow for finding runs of homozygosity outlined in Dr. Lencz’s paper. |
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Advanced |
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Analyzing RNA Sequence DataThe following tutorial is designed to systematically introduce you to a number of techniques for analyzing your RNA-Seq or other high throughput sequencing data output within SVS. It is not meant to replicate all the workflows you might use in a complete analysis, but instead touch on a sampling of the more typical scenarios you may come across in your own studies. |
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CNV - Quality AssuranceThis tutorial covers a typical workflow for quality assurance procedures for whole genome CNV analysis. It also includes some discussion of importing and processing raw data files prior to beginning a CNV analysis project. The tutorial is built around the Affymetrix 500K array, but the workflows are generally applicable to most genotyping arrays and aCGH platforms. There are some anomalies with Illumina data where certain analysis steps may not directly apply. |
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Copy Number Variation (CNV) Univariate AnalysisThis tutorial covers a basic workflow for whole genome CNV analysis and association testing using the univariate segmentation process in SVS. The tutorial is built around the Affymetrix 500K array, but the workflows are generally applicable to most SNP microarray platforms as well as most aCGH platforms. There are some anomalies with Illumina microarray data where certain analysis steps may not directly apply. |
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CNV PCA SearchThis tutorial leads you through a holistic approach to determine the optimal number of principal components to correct for with copy number data by utilizing both PCA and association analysis techniques. |
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Creating a Genome MapCurrently 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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Finding the Causal Variant of a Novel X-Linked DisorderThis tutorial covers an advanced workflow that aims to find the causal variant in the X-linked fatal disorder, Ogden Syndrome. Several filtering procedures are applied to the family data that narrow down the variant set based on our knowledge of the syndrome. |
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NGS Family AnalysisThis tutorial covers a comprehensive NGS family-based analysis workflow. The tutorial assumes prior filtering to narrow the variant set to rare and functional variants. |
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Rare Variant Analysis of Complex DiseasesThis tutorial covers a complex case/control variant analysis workflow. The steps include variant collapsing and association testing using sequence data and a simulated phenotype. |
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Recalling Genotypes with BEAGLECALLThis 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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Variant Filtering on Unrelated SamplesThis tutorial covers a comprehensive filtering workflow to narrow down a variant set to damaging nonsynonymous rare variants. The dataset used in this tutorial has been filtered down to exon regions where at least one sample has a variant. |
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Fundamentals |
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Getting Started with SVSThis video tutorial introduces you to the SVS interface and methodically takes you through starting your own project including exploring drop-down menus, and plotting association results. Access the Video Tutorial » | Runtime: 20 minutes |
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|
Introduction to SVS 7: Importing, combining datasets, spreadsheet manipulation, and filteringThis tutorial seeks to guide you through basic importing and spreadsheet manipulation. The steps outlined aim to make you a power user by providing examples of functions that are often under-utilized but can make spreadsheet manipulation a breeze. |
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SNP Genome-Wide AssociationThe following tutorial is designed to systematically introduce you to a number of techniques for genome-wide association studies. It is not meant to replicate all the workflows you might use in a complete analysis, but instead touch on a sampling of the more typical scenarios you may come across in your own studies. |
|
|
VIDEO: Genome-Wide SNP AssociationThe following short tutorial covers an abbreviated SNP analysis workflow on a whole-genome scale. Access the Video Tutorial » | Runtime: 9 minutes |
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Intermediate |
||
|
LD and Haplotype AnalysisThis 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. |
|
|
Quantitative Haplotype Association and Haplotype Trend RegressionThis tutorial provides a step-by-step workflow for generating haplotype frequency tables from and LD plot of your genotype data and then using those tables to perform numerical association or regression. |
|
|
VIDEO: Quantitative Haplotype Association and Haplotype Trend RegressionThis tutorial provides a step-by-step workflow for creating an LD plot from a marker mapped spreadsheet, defining a haplotype block for a region of interest, and generating haplotype frequency tables for that block. Access the Video Tutorial » | Runtime:2:35 |
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Regression with CovariatesThis tutorial provides an in-depth look at the regression capabilities in SVS. It will cover controlling for confounding variables, model comparison, and stepwise regression. The genotype spreadsheet included in the project file contains PCA-corrected numeric SNP columns for an additive model. The phenotype information is simulated. |
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Runs of Homozygosity AnalysisUsing a simulated dataset, this tutorial will lead you step-by-step through the workflow for finding runs of homozygosity outlined in Dr. Lencz’s paper. |
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Advanced |
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Creating a Genome MapCurrently 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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Recalling Genotypes with BEAGLECALLThis 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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Fundamentals |
||
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Getting Started with SVSThis video tutorial introduces you to the SVS interface and methodically takes you through starting your own project including exploring drop-down menus, and plotting association results. Access the Video Tutorial » | Runtime: 20 minutes |
|
|
Introduction to SVS 7: Importing, combining datasets, spreadsheet manipulation, and filteringThis tutorial seeks to guide you through basic importing and spreadsheet manipulation. The steps outlined aim to make you a power user by providing examples of functions that are often under-utilized but can make spreadsheet manipulation a breeze. |
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Intermediate |
||
|
Introduction to DNA-SeqThis tutorial covers the introductory steps and procedures that will prepare your dataset for further NGS analysis and filtering. The steps include data import, annotation track download and filtering, and variant classficiation. |
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Advanced |
||
|
Creating a Genome MapCurrently 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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Finding the Causal Variant of a Novel X-Linked DisorderThis tutorial covers an advanced workflow that aims to find the causal variant in the X-linked fatal disorder, Ogden Syndrome. Several filtering procedures are applied to the family data that narrow down the variant set based on our knowledge of the syndrome. |
|
|
NGS Family AnalysisThis tutorial covers a comprehensive NGS family-based analysis workflow. The tutorial assumes prior filtering to narrow the variant set to rare and functional variants. |
|
|
Rare Variant Analysis of Complex DiseasesThis tutorial covers a complex case/control variant analysis workflow. The steps include variant collapsing and association testing using sequence data and a simulated phenotype. |
|
|
Variant Filtering on Unrelated SamplesThis tutorial covers a comprehensive filtering workflow to narrow down a variant set to damaging nonsynonymous rare variants. The dataset used in this tutorial has been filtered down to exon regions where at least one sample has a variant. |
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Fundamentals |
||
|
Getting Started with SVSThis video tutorial introduces you to the SVS interface and methodically takes you through starting your own project including exploring drop-down menus, and plotting association results. Access the Video Tutorial » | Runtime: 20 minutes |
|
|
Introduction to SVS 7: Importing, combining datasets, spreadsheet manipulation, and filteringThis tutorial seeks to guide you through basic importing and spreadsheet manipulation. The steps outlined aim to make you a power user by providing examples of functions that are often under-utilized but can make spreadsheet manipulation a breeze. |
|
Intermediate |
||
|
Comparing Copy Number Variations Between Tumors and Normals Using the Affymetrix MIP ArrayThis 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. |
|
|
Regression with CovariatesThis tutorial provides an in-depth look at the regression capabilities in SVS. It will cover controlling for confounding variables, model comparison, and stepwise regression. The genotype spreadsheet included in the project file contains PCA-corrected numeric SNP columns for an additive model. The phenotype information is simulated. |
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Advanced |
||
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Creating a Genome MapCurrently 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. |
|
|
CNV - Quality AssuranceThis tutorial covers a typical workflow for quality assurance procedures for whole genome CNV analysis. It also includes some discussion of importing and processing raw data files prior to beginning a CNV analysis project. The tutorial is built around the Affymetrix 500K array, but the workflows are generally applicable to most genotyping arrays and aCGH platforms. There are some anomalies with Illumina data where certain analysis steps may not directly apply. |
|
|
Copy Number Variation (CNV) Univariate AnalysisThis tutorial covers a basic workflow for whole genome CNV analysis and association testing using the univariate segmentation process in SVS. The tutorial is built around the Affymetrix 500K array, but the workflows are generally applicable to most SNP microarray platforms as well as most aCGH platforms. There are some anomalies with Illumina microarray data where certain analysis steps may not directly apply. |
|
|
CNV PCA SearchThis tutorial leads you through a holistic approach to determine the optimal number of principal components to correct for with copy number data by utilizing both PCA and association analysis techniques. |
|
Fundamentals |
||
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Getting Started with SVSThis video tutorial introduces you to the SVS interface and methodically takes you through starting your own project including exploring drop-down menus, and plotting association results. Access the Video Tutorial » | Runtime: 20 minutes |
|
|
Introduction to SVS 7: Importing, combining datasets, spreadsheet manipulation, and filteringThis tutorial seeks to guide you through basic importing and spreadsheet manipulation. The steps outlined aim to make you a power user by providing examples of functions that are often under-utilized but can make spreadsheet manipulation a breeze. |
|
Advanced |
||
|
Analyzing RNA Sequence DataThe following tutorial is designed to systematically introduce you to a number of techniques for analyzing your RNA-Seq or other high throughput sequencing data output within SVS. It is not meant to replicate all the workflows you might use in a complete analysis, but instead touch on a sampling of the more typical scenarios you may come across in your own studies. |
|
|
Creating a Genome MapCurrently 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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Fundamentals |
||
|
Getting Started with SVSThis video tutorial introduces you to the SVS interface and methodically takes you through starting your own project including exploring drop-down menus, and plotting association results. Access the Video Tutorial » | Runtime: 20 minutes |
|
Introduction to SVS 7: Importing, combining datasets, spreadsheet manipulation, and filteringThis tutorial seeks to guide you through basic importing and spreadsheet manipulation. The steps outlined aim to make you a power user by providing examples of functions that are often under-utilized but can make spreadsheet manipulation a breeze. |
Intermediate |
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Family-Based AnalysisThis 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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Advanced |
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Creating a Genome MapCurrently 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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