Category Archives: Best practices in genetic analysis

Chelsey Clayton

Top 3 Most Viewed Tutorials from Golden Helix

Tutorials are ever-present in the world today, and for good reason. Why struggle through a complicated process yourself, when there is already a guide established to assist? While no one would suggest that a tutorial is the only way to … Continue reading

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Andreas Scherer

Top 5 Webcasts to Watch at GoldenHelix.com

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, … Continue reading

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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

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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 , , , | 5 Comments
Andrew Jesaitis

The State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP

Up until a few weeks ago, I thought variant classification was basically a solved problem. I mean, how hard can it be? We look at variants all the time and say things like, “Well that one is probably not too … Continue reading

Posted in Best practices in genetic analysis, Technology review | Tagged , , , | 19 Comments
Gabe Rudy

The New Human Genome Reference and Clinical Grade Annotations: It’s All About the Coordinates

On my flight back from this year’s Molecular Tri-Conference in San Francisco, I couldn’t help but ruminate over the intriguing talks, engaging round table discussions, and fabulous dinners with fellow speakers. And I kept returning to the topic of how … Continue reading

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Chelsey Clayton

Public Data? What’s that good for anyway?

Dr. Bryce Christensen recently gave a webcast on Maximizing Public Data Sources for Sequencing and GWAS Studies in which he covered options for getting GWAS and sequence information online, tips for working with these datasets and what you’ll see in … Continue reading

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Guest Post: Finding Rare Pieces of Hay in a Haystack

Utilizing Identical Twins Discordant for Schizophrenia to Uncover de novo Mutations We are living in exciting times – the reality of high-resolution microarrays and individual genome sequencing now offers renewed hope in the search for the causes of complex diseases. … Continue reading

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