Category Archives: How to’s and advanced workflows

Cheryl Rogers

Q&A Surrounding Population-Based DNA Variant Analysis

Last month, Dr. Bryce Christensen presented Population-Based DNA Variant Analysis via webcast. The webcast reviewed the fundamentals of population-based variant analysis and demonstrated some of the tools available in SVS for analysis of both common and rare variants such as the … Continue reading

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Cheryl Rogers

Q&A from our December Genomic Prediction webcast

Our Genomic Prediction webcast in December discussed using Bayes-C pi and Genomic Best Linear Unbiased Predictors (GBLUP) to predict phenotypic traits from genotypes in order to identify the plants or animals with the best breeding potential for desirable traits. The … Continue reading

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Bryce Christensen

SVS, Population Genetics, and 1000 Genomes Phase 3

One frequent question I hear from SVS customers is whether whole exome sequence data can be used for principal components analysis (PCA) and other applications in population genetics. The answer is, “yes, but you need to be cautious.” What does … Continue reading

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Andrew Jesaitis

VarSeq: A bioinformatics Swiss Army knife

If you’ve seen the recent webinars given by Gabe Rudy and Bryce Christensen, you’ve no doubt been impressed by the capabilities of VarSeq when it comes to annotation and filtering. However, we sometimes forget that the power that enables all … Continue reading

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Ashley Hintz

A little known fact about Box Plots

A helpful tool that is included in SVS, but many of our customers may not know about, is the ability to create Box Plots or box-and-whisker plots. These are effective visualizations for comparing groups of numerical data through the data … Continue reading

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Andreas Scherer

Top 5 Webcasts to Watch at GoldenHelix.com

Genomic research is exploding. There is a plethora of new methods and workflows for research and clinical use. While we are a software company at heart, we find ourselves in the role of educators. Our customer interactions are about informing, … Continue reading

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Andrew Jesaitis

Turning SRA Files Into Usable BAMs and VCFs

In our recent webcast, Advancing Agrigenomic Discoveries with Sequencing and GWAS Research, Greta Linse Peterson featured bovine data which she download from the NCBI website. The data was downloaded in SRA format and in order to analyze the data in … Continue reading

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Greta Linse Peterson

Back to Basics: Importing/Exporting Data in Imputation Program Data Formats with SVS

In a recent blog post (Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory Usage), Autumn Laughbaum compared three imputation programs. Data can be exported from, or imported into, SVS in the standard file formats for … Continue reading

Posted in Add-on scripts & data repository, Bioinformatic support, How to's and advanced workflows | 1 Comment
Greta Linse Peterson

Follow Along on an Analyst’s Journey to Filter Whole Genome Data to Four Candidate Variants in SVS

Last week Khanh-Nhat Tran-Viet, Manager/Research Analyst II at Duke University, presented the webcast: Insights: Identification of Candidate Variants using Exome Data in Ophthalmic Genetics. (That link has the recording if you are interested in viewing.) In it, Khanh-Nhat highlighted tools … Continue reading

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Dr. Ken Kaufman’s Webcast on Exome Sequencing Wildly Successful

Thank you to everyone who joined us yesterday for a webcast by Dr. Ken Kaufman of Cincinnati Children’s Hospital: “Identification of Candidate Functional Polymorphism Using Trio Family Whole Exome DNA Data.” Over 750 people registered for this event and 430 … Continue reading

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