How To’s & Advanced Workflows

New Tutorial: VSReports

May 11, 2017

The new VSReports tutorial covers a basic VSReports workflow with an emphasis on understanding and exploring report customizations. This tutorial requires an active VarSeq license with the the VSReport feature included. You can go to Discover VarSeq or email [email protected] to request an evaluation license with the VSReports functionality included. VS Reports provides…

Read more →

New Tutorial: VSWarehouse

Apr 27, 2017

The new VSWarehouse Tutorial covers the basic VSWarehouse workflow.This tutorial focuses on connecting to a VSWarehouse instance from VarSeq, adding an existing VSWarehouse project as an annotation source and using reports and assessment catalogs hosted on VSWarehouse. This workflow requires an active VarSeq license with the VSWarehouse feature included. You can…

Read more →

Adding RSIDs to your SVS marker mapped spreadsheet

Feb 14, 2017

In the new Genotype Imputation tool that is coming soon to SVS, allele encoding is an important part of matching data between the target and the reference panels. If the same platform provider is being used, then A/B encoding can be used. However, it’s better to use the Reference/Alternate allele…

Read more →

Utilizing VSReports in Your Clinical Workflow

Jan 12, 2017

Clinical labs need to be able to process samples down to a short list of variants and publish a professional report. VSReports helps scientists and clinicians alike create timely, actionable reports that can improve clinical decision making and streamline patient care by seamlessly incorporating the results of tertiary analysis into…

Read more →

Using Assessment Catalogs in your VarSeq workflow

Dec 15, 2016

Variant interpretation is an integral part of any workflow that results in some decisions being made about the validity and suspected functional impact of a variant in a given sample and their presenting phenotypes. The VarSeq Assessment Catalog functionality is designed to assist the VarSeq user in streamlining this process.…

Read more →

Exporting Data From VarSeq to Excel

Nov 17, 2016

True to its nature, VarSeq offers multiple data export options. You can export result tables from VarSeq to Text, VCF, a VarSeq annotation file and most importantly an XLSX (Excel) File. VarSeq’s Excel export options provide a lot of flexibility in the information that is exported and preserve the formatting of…

Read more →

How To Annotate and Filter Variants in SVS

Oct 20, 2016

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…

Read more →

Determining the best LD Pruning options

Sep 13, 2016

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…

Read more →

Webcast on Big Data in Genomics

Sep 8, 2016

Wednesday, September 21st @ 12:00 pm EDT Every day, the trove of genomic data is growing. Clinics are sequencing targeted genes at high read depths to report out genetic tests. Research groups are adding new exomes and genomes to their disease-specific cohorts. Agricultural breeders are genotyping their herds and flocks…

Read more →

FAQ: Creating Repeatable Clinical Workflows

Aug 18, 2016

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…

Read more →

Compute Kinship Matrices & GBLUP on Very Large Sample Sets

Aug 2, 2016

Now available in SVS! Increasingly important in the analysis of the genotype to phenotype relationship is accurately accounting for the relatedness of samples. This is especially important to model correctly in plant and animal populations where man-directed breeding shapes the relationship structure. Along with trait association, one of the high-value…

Read more →

Our 5 Most Watched Webcasts

Jul 21, 2016

Every month hundreds of clinicians and researchers access the variety of free resources on the Golden Helix website. Our resource library hosts eBooks, webcasts and tutorials to keep the community apprised of new methods, informed on best practices and to help our customers get the most out of their software purchase.…

Read more →

VSPipeline Tips and Tricks

Jun 2, 2016

The power of VSPipeline is in it’s ability to automate VarSeq workflows, streamlining everything from variant filtering to clinical reporting. Using VarSeq to create a pipeline template is great because it allows you to dial in the applied filters as well as interactively organize the annotations and applied algorithms. Automating…

Read more →

Customizing Workflows for Family Structure

May 12, 2016

During the webcast yesterday, I demonstrated a few ways of customizing de Novo Candidate and Compound Heterozygous Candidate workflows to consider family structure that was slightly different from the default trio workflow. The families included additional affected and unaffected siblings added to a trio as well as looking at what…

Read more →

Custom Family Workflows featured in May Webcast

Apr 26, 2016

Wednesday, May 11th 12:00 pm EDT VarSeq contains default workflows for Trio analysis which include filter chains for identifying de Novo and Compound Heterozygous variants, but what if you have data for a full Quad or even just a few siblings? How could your VarSeq workflow be adjusted to handle…

Read more →

Clinical Reports – New & Improved Templates!

Apr 14, 2016

Clinical reports come in all shapes, sizes and flavors. With that in mind, our clinical reporting interface VSReports was built to be highly customizable and flexible.  With a little Javascript and HTML know-how, your clinical reports can be customized to meet the needs and goals of your lab. With a little…

Read more →

Genotyping by Sequencing (GBS) Workflows in SVS

Mar 29, 2016

Did you know you can analyze your Genotyping by Sequencing (GBS) data in SVS? Well you can! You can combine tools for both GWAS quality control and analysis with tools for NGS data analysis to either identify SNPs in your dataset or to identify differences between populations or sub-species. If…

Read more →

Compound Heterozygous Workflows: Including a 2nd Affected Child

Feb 2, 2016

Compound Heterozygous Workflows: Including a 2nd Affected Child Looking for Compound Heterozygous regions for a trio is fairly straight forward in VarSeq, we include this workflow in our shipped Exome Trio Template. An example of which is included with our Example Projects which can be found by going to File…

Read more →

GWAS Example Project Updated for SVS Viewer

Jan 26, 2016

With the release of our updated GWAS E-book, we have recently updated the GWAS example project (SNP Genome-Wide Association Tutorial – Complete). This updated project includes more details about how spreadsheets were generated, how to generate plots and which images were used for the GWAS E-book. This information can be found…

Read more →

GWAS eBook – 2nd Edition

Jan 12, 2016

I hope your 2016 is off to a good start! We at Golden Helix have been busy preparing and planning new and updated content for the community. First up is an updated GWAS ebook which includes a sample Meta-analysis example project. In the 2nd edition, we start with an introduction…

Read more →