Category Archives: How to’s and advanced workflows

Bryce Christensen

Tumor/Normal Pair support now available in VarSeq!

VarSeq now supports analysis of paired Tumor/Normal samples! Tumor/Normal support has been one of the most common feature requests for VarSeq since it was launched late last year, and we are excited to make this functionality available to all of … Continue reading

Posted in How to's and advanced workflows, News, events, & announcements | Tagged , | Leave a comment
Ashley Hintz

Comparing Variants using a Venn Diagram

One of the lesser known functions in SVS allows the user to create Venn diagrams comparing variants found in multiple spreadsheets. These different spreadsheets could come from individuals samples, a case vs. control group or several variant databases. It is … Continue reading

Posted in How to's and advanced workflows | Tagged , | Leave a comment
Bryce Christensen

Looking Beyond the Exons: Splice Altering Variants

There are many approaches that one might use to define a variant as potentially deleterious. For example, we often see analysis workflows based on rare, non-synonymous variants, perhaps incorporating additional annotation sources that capture known or predicted consequences of coding … Continue reading

Posted in Best practices in genetic analysis, How to's and advanced workflows | 1 Comment
Cheryl Rogers

VarSeq as a Clinical NGS Platform Q&A

Our VarSeq as a Clinical Platform webcast last week highlighted some recent updates in VarSeq that support gene panel screenings and rare variant diagnostics. The webcast generated some good questions, and I wanted to share them with you. If the … Continue reading

Posted in Customer Questions, How to's and advanced workflows | Tagged , , | Leave a comment
Ashley Hintz

Visually Filtering Data in GenomeBrowse

Over 650 GenomeBrowse licenses have been registered and downloaded since the beginning of 2015, and with so many people enjoying the utility of this freeware program, I wanted to showcase some advanced tips and tricks so you can get more … Continue reading

Posted in How to's and advanced workflows, Uncategorized | Tagged | 1 Comment
Ashley Hintz

Analyzing a Unique Family Structure in VarSeq 1.1.1

I am constantly on the lookout for fun or interesting datasets to analyze in SVS or VarSeq and recently came across a study looking into inherited cardiac conduction disease in an extended family (Lai et al. 2013). The researchers sequenced … Continue reading

Posted in Clinical genetics, How to's and advanced workflows | Tagged , , | 1 Comment
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

Posted in Best practices in genetic analysis, Customer Questions, How to's and advanced workflows | Tagged , , , | Leave a comment
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

Posted in Best practices in genetic analysis, Customer Questions, How to's and advanced workflows | Tagged , , , | Leave a comment
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

Posted in Customer Questions, General statistical genetics principles, How to's and advanced workflows | Tagged | Leave a comment
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

Posted in How to's and advanced workflows, Technology review | Tagged | Leave a comment