Category Archives: How to’s and advanced workflows

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 variants. Annotations for coding regions of the genome are relatively abundant and familiar to genome scientists. We are comfortable in… Read more »

VarSeq as a Clinical NGS Platform Q&A

CNV User

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 questions below spark new questions or need clarification, feel free to get in touch with us at info@goldenhelix.com. Question: Should… Read more »

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 out of GenomeBrowse! Under the Controls panel, when you’re clicked inside a data plot, there is a “Filter” tab. This… Read more »

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 »