Author Archives: Golden Helix

Announcing Technical Support Bulletins

         July 20, 2012

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 one of Illumina’s bulletins and realized that was exactly what we needed at Golden Helix as well! On Wednesday, we… Read more »

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

         July 16, 2012

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 will find descriptions of the new tools and the related annotations track(s).

New Analysis and Spreadsheet Manipulation Tools in SVS!

         June 28, 2012

The script development team at Golden Helix has been hard at work these past few months and this means several new and exciting tools for our SVS customers!  The scripts featured in this blog post vary in function, from expanding the analytical options currently offered in SVS to transforming and editing spreadsheets.  As always, we invite you to visit our… Read more »

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

         June 27, 2012

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 this point have already seen several emails from me this year! Email is certainly one way to get an announcement… 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 »

How SVS Treats Gender in Calculating Genotype Statistics

         May 9, 2012

Recently several customers have asked how SNP & Variation Suite (SVS) treats gender when calculating genotype statistics. In this blog post, I will cover SVS’ current capabilities, what we have available through Python scripts, and what is coming in the near future. We thank all of our customers who have inquired about these capabilities and have given us valuable feedback… Read more »

New Features in SVS: Accounting for Sex Chromosomes and Filter Columns by Variant Type

         February 29, 2012

In the last couple of weeks, the SVS Script Repository has seen a handful of new additions.  This blog post highlights three new scripts, but as always, we welcome you to check out our repository regularly to enjoy the new and exciting functionality made possible by our Python integration in SVS! (To get these, or any other scripts, simply go… Read more »

Admixture and Blaine Bettinger

         January 25, 2012

Allow me to introduce you to Blaine Bettinger.  Blaine is a patent attorney who holds a PhD in Biochemistry with a concentration in genetics.  He is also a family history enthusiast who writes the Genetic Genealogist blog, where he gives commentary on applications of genomic science for advancing personal and family history research.  I first learned about Blaine last May… Read more »

New Plant/Animal Genomes and Annotation Tracks Now Available

         December 8, 2011

Recently we have expanded our annotation track offerings with new human variant frequency catalogs such as the 1000 Genomes Phase 1 Data. Of course, we also curate data for plant and animal genomes – some of which are currently available in our software and some of which will be available in our next release. In this blog post, I will… Read more »

Wondering what SVS can do for a PhD student? Just ask Sander.

         September 14, 2011

Sander van der Laan is like many Ph.D. students in the genomic analysis space. He has a lot of data and a lot of ideas about how to analyze it. His professor wants results. He’s the only one doing genetics (everyone else in his department is doing proteomics), so there’s always too much to do. And he finds command-line tools… Read more »

Marker Map Manipulation Improvements in SVS 7.5

         August 31, 2011

Manipulating a marker map in SVS has never been easier, thanks to expanded functionality in SVS 7.5.  Have you ever wanted to view annotation data next to marker map data?  Or expand the current marker map with spreadsheet data to create a custom map?  SVS 7.5 features two new functions that can accomplish these tasks. Adding Annotation Data to a… Read more »

Please Help Me Get My Regression Model Set Up!

         July 6, 2011

Golden Helix’ SNP & Variation Suite (SVS) has a Regression Module to enable researchers with varying degrees of statistical knowledge to interrogate their data using regression models to account for potential confounding effects of covariates and interaction terms. While these tools are labeled “basic”, they can be difficult to use and results hard to interpret for those who have only… Read more »

Going Coast to Coast for the Latest NGS News

         June 23, 2011

Last week I was able to attend two very interesting conferences about the latest developments in the analysis of sequence data.  I started the week in San Diego at the Illumina iDEA Conference and finished it in Philadelphia at Children’s Hospital of Philadelphia’s (CHOP) Third Annual Next-Generation Sequencing Symposium.  The Illumina conference was an opportunity to learn about the latest… Read more »

Updates to CNAM Make SVS the Fastest and Most Accurate Copy Number Tool for Common and Rare CNVs

         March 16, 2011

A recent email from a user of SVS: “Your CNAM Optimal Segmentation algorithm is by far the best I ever used and believe me, I’ve tried many. Great use of the GPU for segmentation – it is 3x faster than using my 8 CPUs alone and 25x faster compared to 1 CPU.” SNP & Variation Suite (SVS) version 7.4 introduced… Read more »

Getting Your Research Questions Answered Quickly with the Various Golden Helix Support Mediums

         March 9, 2011

From the Customer Support Desk… At Golden Helix, we place a strong emphasis on customer support and helping our customers use the software to the best of their abilities to answer any research questions they have. Due to such a strong emphasis on customer and technical support, there are numerous sources of help available. These include the low tech option… Read more »

ANOVA, Nonparametric Tests, and More Added to SVS via New Python Capabilities

         March 3, 2011

Our recent blog post about the release of  SNP & Variation Suite v7.4 gave you a sneak peek into what can be achieved with the revamped SVS/Python integration, which includes the incorporation of NumPy and SciPy libraries and new graphical layout capabilities. A Python package (such as SciPy) is similar to an R package, which you may be more familiar… Read more »

Recent Publications on Asthma, Schizophrenia, Peripheral Neuropathy, Rheumatoid Arthritis, Alzheimer Disease, and Esophageal Cancer

         February 17, 2011

As you may have guessed from the title of this post, we’ve had a lot of customers publishing in the first six weeks of 2011. We are always excited to hear about about our customers’ findings and how they were able to use SNP & Variation Suite to accelerate their research. (All abstracts below.) First, in the pharma world, congrats… Read more »

CNV Analysis Tips for Illumina Data

         November 24, 2010

Please see our updated tutorials for CNV Analysis by visiting: http://goldenhelix.com/resources/SNP_Variation/tutorials/index.html The following statement is representative of a common question that is posed to the Golden Helix support team: “I followed all of the steps in the SVS7 CNV analysis tutorial, but my results seem kinda funny. The segment means are skewed to the left and it doesn’t look like… Read more »