Category Archives: How to’s and advanced workflows

VSWarehouse Updates with the Power of VarSeq 1.4.7

VSWarehouse Updates

With the recent release of VarSeq 1.4.7, we have expanded the concepts of our popular assessment catalog to include CNV and other region-based records and not just variants. To match these capabilities, we have made a major update to VSWarehouse that supports these new record types in the centrally hosted and versioned Catalogs and Reports. Review of the VSWarehouse Genomic… Read more »

New VarSeq Single Exome Demo Project

single exome

As VarSeq is quickly becoming the go-to variant analysis software for tertiary analysis, we want to give our readers the opportunity to examine completed projects from start to finish. As an addition to the currently available demonstration projects, we are pleased to provide users with a Single Exome Analysis example project. To access this project simply click here to download… Read more »

Annotation Education Series: Clinical Assessment Tracks

Clinical Assessment Tracks Golden Helix provides a large catalog of annotation sources for our research and clinical clientele. Making these public data repositories available to all our users is no easy task. As Cody Sarrazin mentioned in his blog post, annotation curation is a complex data science pipeline. This process aggregates data from many disparate sources and normalizes it into… Read more »

Upcoming Webcast: Comprehensive Clinical Workflows for Copy Number Variants in VarSeq

Tumor Sequencing

September 27, 2017 12:00 PM, EDT While Copy Number Variants are important to detect and interpret in many clinical genetic tests, labs have been without a comprehensive solution that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants. Golden Helix has developed and validated with our clinical partners a specialized NGS-based CNV caller capable of detecting… Read more »

Frequently Asked Questions: CNV analysis in VarSeq

CNV FAQ

The support team at Golden Helix is always here to help with your SVS and VarSeq needs. Often, we receive some excellent questions that should be shared with the rest of our users. This blog will answer some common questions we’ve been seeing lately regarding VarSeq CNV. I’ve noticed there is a version 2 of the CNV caller on Targeted Regions Algorithm, how has… Read more »

Understanding Your GWAS Signal with LD Scores

Genome-Wide Association Studies

When studying complex diseases that may have multi-genic contributions from across the genome, it is not uncommon to see what may appear like elevated correlation between your trait or other test variable and the SNPs across the genome. The problem is at first glance you won’t be able to tell if this is due to a population structure in your… Read more »

Cancer Gene Panels Tutorial

cancer gene panel tutorial

VarSeq enables breakthrough discoveries in cancer diagnostics by supporting gene panel testing and whole exome and genome analysis. We wanted to share our Cancer Gene Panel tutorial which covers a basic gene panel workflow with an emphasis on adding, modifying and manipulating filter chains. This tutorial will start with creating a new project from an empty project template, importing data, creating… Read more »

New Tutorial: VSReports

      Darby Kammeraad    May 11, 2017    No Comments on New Tutorial: VSReports
cancer gene panel tutorial

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 info@goldenhelix.com to request an evaluation license with the VSReports functionality included. VS Reports provides the ability to generate clinical-grade reports. This feature enables VarSeq… Read more »

New Tutorial: VSWarehouse

      Darby Kammeraad    April 27, 2017    No Comments on New Tutorial: VSWarehouse
cancer gene panel tutorial

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 go to Discover VarSeq or email info@goldenhelix.com to request an… Read more »

New Tutorial: VarSeq CNV Caller

cancer gene panel tutorial

The new VarSeq CNV Caller Tutorial covers the basics of the VarSeq CNV calling algorithm, with an emphasis on visualization and interpretation of results. This workflow requires an active VarSeq license with the CNV Caller on Target Regions feature included. You can go to Discover VarSeq or email info@goldenhelix.com to request an evaluation license with the CNV functionality included. The… Read more »

Adding RSIDs to your SVS marker mapped spreadsheet

VarSeq Updated

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 encoding associated with AGCT format to ensure accuracy. If an… Read more »

Utilizing VSReports in Your Clinical Workflow

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 a customizable clinical report. To include the VSReports functionality in… Read more »

Using Assessment Catalogs in your VarSeq workflow

Variant Assessment Cataloug

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. To include this functionality in your workflow, you will first… Read more »

Exporting Data From VarSeq to Excel

CNV FAQ

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 data during the export process from VarSeq to Excel. This… Read more »

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 »

CADD, OMIM and OncoMD added to SVS

CAD, OMIM and OncoMD

In our SVS 8.6.0 release, we updated our Annotate and Filter Variants feature to utilize our powerful VarSeq annotations. Annotations can be run against gene, interval, variant, and tabular tracks, including RefSeq, ClinVar, CADD, OMIM and OncoMD. The new streamlined dialog allows users to select track specific options and to set up custom filters. While our public annotation repository has… 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 »

Webcast on Big Data in Genomics

      Delaina Hawkins    September 8, 2016    No Comments on Webcast on Big Data in Genomics

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 by the thousands of thousands. The conventional attitude to big… 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 »

Compute Kinship Matrices & GBLUP on Very Large Sample Sets

Binary Data

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 use cases for genotyping animals and plants is to estimate… Read more »