How To’s & Advanced Workflows

Tumor-normal demo project comes to VarSeq

Dec 1, 2015

With the release of VarSeq 1.3.1 we have included a new demo project to showcase a single tumor-normal pair analysis workflow. The project can be accessed through VarSeq and VarSeq Viewer by going to File > Open Example Projects > Example Tumor-Normal Pair Analysis. This project contains an exome pair…

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A New and Unexpectedly Powerful VarSeq Feature

Nov 17, 2015

With the release of VSReports, we added the ability to “select” rows of your filtered output (often variants, but potentially things like coverage regions or genes) with a new feature dubbed “Record Sets”, but more often described as “colored checkboxes” for your tables. Although necessary for the important task of…

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Try out SVS for Free!!

Nov 10, 2015

Give our SVS viewer a try today! Interested in seeing what the SNP & Variation Suite (SVS) software can do? Download the free SVS Viewer! With the SVS Viewer, you can explore and interact with the workflows of a pre-built projects. To get you started, we have included a SNP GWAS…

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Analyzing a Single Sample Exome in VarSeq

Oct 22, 2015

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…

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GxE Regression Option to be Available in SVS

Aug 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…

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Coverage Statistics Come to VarSeq

Aug 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…

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Tumor/Normal Pair support now available in VarSeq!

Jul 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…

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Comparing Variants using a Venn Diagram

Jul 7, 2015

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…

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VarSeq as a Clinical NGS Platform Q&A

Apr 21, 2015

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…

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Visually Filtering Data in GenomeBrowse

Apr 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…

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Analyzing a Unique Family Structure in VarSeq 1.1.1

Mar 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…

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Q&A from our December Genomic Prediction webcast

Feb 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…

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SVS, Population Genetics, and 1000 Genomes Phase 3

Jan 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…

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VarSeq: A bioinformatics Swiss Army knife

Dec 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…

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A little known fact about Box Plots

Oct 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…

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Turning SRA Files Into Usable BAMs and VCFs

Jan 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…

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

Dec 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…

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

Mar 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…

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

Aug 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…

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Why You Should Care About Segmental Duplications

Jun 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…

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