Category Archives: How to’s and advanced workflows

Analyzing a Single Sample Exome in VarSeq

         October 22, 2015
Exome

While VarSeq comes with a number of starter workflows that are stored as templates, customers also have the option of creating filter chains from scratch; analyzing a single exome may require you to do exactly that. In this blog, I’ll go through analyzing a single exome and generating a list of variants for further study. After importing the variant data… Read more »

GxE Regression Option to be Available in SVS

         August 26, 2015

We are pleased to announce that another one of the most asked for features is going to be a part of our SNP & Variation Suite™ software, Gene by Environment Interaction Regression (also known as GxE Regression). Earlier this year other highly asked for features were added to SVS including applying a prediction model to a new dataset, cross-validation for… Read more »

Coverage Statistics Come to VarSeq

         August 20, 2015

A prerequisite for clinical NGS interpretation is ensuring that the data being analyzed is of high enough quality to support the test results being returned to the physician. The keystone of this quality control process is coverage analysis. Coverage analysis has two distinct parts. Ensure that there is sufficient coverage to be confident in called variants Make certain that no… Read more »

Tumor/Normal Pair support now available in VarSeq!

         July 16, 2015

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 our VarSeq users in the latest update (version 1.1.4). VarSeq is a powerful platform for annotation and filtering of DNA… Read more »

Comparing Variants using a Venn Diagram

         July 7, 2015
annotate

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 a helpful tool for visually comparing different variants. Start by creating spreadsheets for each group/samples you’d like to compare. The… Read more »

Looking Beyond the Exons: Splice Altering Variants

         June 5, 2015

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

         April 21, 2015
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

         April 16, 2015

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

         March 12, 2015

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

         February 17, 2015

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

         February 12, 2015

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

         January 27, 2015

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

         December 5, 2014

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 »

A little known fact about Box Plots

         October 16, 2014

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 quartiles. I’ll take you through a couple different cases with examples.

Top 5 Webcasts to Watch at GoldenHelix.com

         August 26, 2014

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, teaching, and consulting. A few years back, we started with regular webcasts that took this idea to the next level…. Read more »

Turning SRA Files Into Usable BAMs and VCFs

         January 21, 2014

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 SVS, the files had to be converted to BAMs and then merged into a single VCF file. Since many of… Read more »

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

         December 31, 2013

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 these and other imputation programs. The goal of this blog post will be to review the different tools available to… Read more »

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

         March 14, 2013

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 available in SVS that might be under used or were recently updated. These tools were used in his last three… Read more »

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

         August 9, 2012

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 attended – a new Golden Helix record! If you missed the webcast (or would like to watch it again), the… Read more »

Why You Should Care About Segmental Duplications

         June 6, 2012

My work in the GHI analytical services department gives me the opportunity to handle data from a variety of sources.  I have learned over time that every genotyping platform has its own personality.  Every time we get data from a new chip, I tend to learn something new about the quirks of genotyping technology.  I usually discover these quirks the… Read more »