Category Archives: Bioinformatic support

Gabe Rudy

Accurate Annotations: Updates to the NHLBI Exome Sequencing Project Variant Catalog

Since its early release in early 2012, the population frequencies from the GO Exome Sequencing Project (ESP) – from the National Heart, Lung and Blood Institute (NHLBI) have been a staple of the genomic community. With the recent release of … Continue reading

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Andreas Scherer

Genetic Testing for Cancer

In 1914 the German cytologist Theodor Boveri coined the phrase “Cancer is a disease of the genome”. At this time his ideas were equally revolutionary as they were highly contested. Fast forward. More than hundred years later, Next-Generation Sequencing effectively … Continue reading

Posted in About GHI, Best practices in genetic analysis, Bioinformatic support, Clinical genetics | Tagged , , | Leave a comment
Ashley Hintz

Analyzing Whole Exome, Large-n Cohorts in SVS

It’s come to my attention in recent weeks, through various customer interactions, that many are not aware of the fantastic functionalities that exist in SNP and Variation Suite (SVS) for large-n DNASeq workflows; this includes large cohort analyses with case/control … Continue reading

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Gabe Rudy

6 Population Catalogs Compared with the ExAC 61,486 Exomes

To say the announcement of Dan MacArthur’s group’s release of the Exome Aggregation Consortium (ExAC) data was highly anticipated at ASHG 2014 would be an understatement. Basically, there were two types of talks at ASHG. Those that proceeded the official … Continue reading

Posted in Big picture, Bioinformatic support, Clinical genetics, Uncategorized | Tagged , , , , | 6 Comments
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 , , , | 6 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
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