Category Archives: How to’s and advanced workflows

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 the exomes from five family members including three affected siblings and their unaffected mother and an unaffected child of one… Read more »

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 SKAT-O method, as well as other functions for annotation, visualization, quality control and statistical analysis of DNA sequence variants. Here… Read more »

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 webcast generated a lot of good questions as our webcasts generally do. I decided to begin to share these Q&A… Read more »

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 cautious mean? Let’s take a look at the 1000 Genomes project for some examples.

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 this complex analysis can also be used in more mundane tasks like VCF subsetting. And although these day-to-day tasks don’t… Read more »