Category Archives: Bioinformatic support

Andreas Scherer

Leveraging SVS for NGS Workflows

Over the last decade, DNA sequencing has made vast technological improvements. With the cost of sequencing decreasing significantly, sequencing technology has become a product for the masses. The sequencing technology and programs that were once used exclusively by major research … Continue reading

Posted in Best practices in genetic analysis, Big picture, Bioinformatic support, Clinical genetics, Uncategorized | Tagged , , , , , , | Leave a comment
Gabe Rudy

RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care

You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product. But in … Continue reading

Posted in Best practices in genetic analysis, Big picture, Bioinformatic support, General statistical genetics principles, Technology review, Uncategorized | Tagged , , , | 3 Comments
Alison Figueira

Runs of Homozygosity Updated

For the SVS 8.2 release we decided to improve upon the existing ROH feature. The improvements include new parameters to define a run and a new clustering algorithm to aide in finding more stringent clusters of runs. The improvements were … Continue reading

Posted in Best practices in genetic analysis, Bioinformatic support | Tagged , , , , | Leave a comment
Bryce Christensen

Have you ever had a bad experience with a VCF file?

“Who has ever had a bad experience with a VCF file?” I like to ask that question to the audience when I present data analysis workshops for Golden Helix. The question invariably draws laughter as many people raise their hands … Continue reading

Posted in Best practices in genetic analysis, Bioinformatic support, Customer Questions | Tagged , , , | 4 Comments
Ashley Hintz

The Differences Between EMMA and EMMAX

I recently gave a webcast on GWAS in a model organism: Arabidopsis thaliana; a question was brought up about the differences between EMMA and EMMAX and why the results with each would differ.

Posted in Bioinformatic support, Customer Questions | Tagged , , , | 1 Comment
Greta Linse Peterson

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

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 … Continue reading

Posted in Add-on scripts & data repository, Bioinformatic support, How to's and advanced workflows | 1 Comment

SVS Workflow Automation Webcast: Your Questions Answered

Last week, we presented a webcast on Workflow Automation in SVS. If you were unable to attend, a recording of it is on our website: http://www.goldenhelix.com/Events/recordings/making-ngs-data-analysis-clinically-practical/index.html In this post I’ll respond to some of the questions we were unable to … Continue reading

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Greta Linse Peterson

Announcing Technical Support Bulletins

Last month I was inspired to create a new way to keep our customers apprised of the latest information on Golden Helix software without cluttering inboxes and overwhelming our blog. I happened to receive a link to an article for … Continue reading

Posted in Bioinformatic support | 2 Comments

New 1kG, dbNSFP, and ESP6500 Annotation Tracks and Associated Filters

SVS 7.6.7 features new tools for filtering sequencing data based on functional predictions and allele frequencies. To complement these new features, new annotations tracks have been uploaded to our data server and are now available for our customers! Below you … Continue reading

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Greta Linse Peterson

New Technical Support Bulletins (Forthcoming!), and a Known Bug with Filter Samples by Call Rate

As Product Quality Manager, I have been spending quite a bit of time lately thinking about the best way to communicate with our Golden Helix customers with regards to product quality and customer support issues. Most of our customers at … Continue reading

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