Author Archives: Steven Hystad

Steven Hystad

About Steven Hystad

Steve Hystad joined the Golden Helix development team in November of 2016 as a Field Application Scientist. Prior to that, Steve worked as a Regulatory Affairs Specialist and Molecular Biologist. Steve earned his Masters in Plant Genetics from Montana State University in 2014. As an FAS, Steve works on data curation, customer support and VSReports. When not working, Steve is skiing, hiking, rafting or searching for Forrest Fenn's treasure.

How To Annotate and Filter Variants in SVS

annotate

The new Annotate and Filter algorithm is now available with the release of SVS 8.6.0, see the release notes for full details on all new and updated features. To access this new functionality, you simply need to update your SVS installation to the new version. The update can be done by clicking the Update Available link at the bottom of… Read more »

Determining the best LD Pruning options

LD Pruning

Pruning your data based on Linkage Disequilibrium (LD) values is an important quality assurance step for GWAS analysis. In particular, some tests such as Identity by Descent Estimation (IBD), Inbreeding Coefficient Estimation (f) and Principal Component Analysis (PCA) will obtain better results if the markers used are not in linkage disequilibrium with each other. Therefore, Golden Helix’s SVS provides the… Read more »

FAQ: Creating Repeatable Clinical Workflows

Repeatable clinical workflows

Question: Now that I’ve added annotation sources for my sample, filtered down to a list of interesting variants, flagged those variants and generated a clinical report, can I save or copy the annotation sources and filters for use on another sample? Short Answer: Yes! Long Answer: VarSeq was created with ease and efficiency in mind. In VarSeq, once you’ve defined… Read more »

Custom Filtering using ClinVar Annotations

ClinVar

ClinVar is one of our most used annotations sources for a variety of workflows. It is also the public annotation source that is updated most frequently of all the sources currently supported in VarSeq. ClinVar provides new versions of their database once a month in several formats (XML, VCF, TXT). We use custom Python scripts to convert the provided VCF… Read more »

Whole Exome Sequencing workflows in VarSeq

Whole Exome Sequencing Workflows

Whole exome sequencing workflows using SNP & Variation Suite (SVS) was presented in a recent webcast, by Dr. Robert Hamilton from the Hospital for Sick Kids. In particular, he performed some filtering on his data to look for only heterozygous variants in his sample of interest, removed variants with allele frequency less than 0.005% based off of the ExAC Variant Frequency… Read more »