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 »
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 »
As most in the Golden Helix community are aware, SNP & Variation Suite (SVS) can handle all sorts of data including files from Affymetrix, Illumina, Agilent, and Complete Genomics with its powerful data management capabilities. Announced in February, SVS is now part of the Pacific Biosciences Partner Program and has the ability to analyze PacBio files.
If you have ever worked with NGS variant data, you may have come to realize that the first task at hand is the seemingly simple categorization of your variants into two bins: known and novel. Of course, if you’ve ever worked with NGS variant data, you may have also come to the realization that this step is more complex than… Read more »
Speaking as somebody with a long history in data analysis, there are few things I find more exciting and tantalizing than new analysis methods that might apply to a problem I am trying to solve or was unable to solve in the past. Whenever I make a breakthrough in one project, I find I want to abandon the current project… Read more »
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 »
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 »
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 »