Tag Archives: Clinical workflows

Automating & Standardizing Your NGS Workflow: Part IV

We have covered a lot of ground in this Automating & Standardizing Your Workflows blog series. First, we saw how to perform secondary analysis with Sentieon to generate the necessary VCF and BAM files for tertiary analysis in Part I. The implementation of VSPipeline allowed for rapid import and project generation for a predefined cancer gene panel project template in… Read more »

Automating & Standardizing Your NGS Workflow: Part III

In our last part of this series, we showed how to run a pre-built workflow template via VSPipeline to automatically import and filter sample variants to streamline the search for clinically relevant variants. Now, we can deep-dive into our filtered, pathogenic variants to fully understand and capture their final classification and interpretation. Filtered Germline Variants for ACMG Guidelines The VSPipeline… Read more »

Automating & Standardizing Your NGS Workflow: Part II

VSPipeline: Automating your Tertiary Workflows The first part of this “Automating & Standardizing your NGS Workflow” blog series covered the secondary analysis steps of read alignment and variant calling with Sentieon. The next step is to transition into the tertiary analysis via utilization of our workflow automation tool, VSPipeline. VSPipeline operates as a command-line tool meant to simplify the deployment… Read more »

Automating & Standardizing Your NGS Workflow: Part I

Secondary Analysis with Sentieon: Rapid and Accurate Variant Calling This blog post will cover the utilization of secondary analysis tools to produce a list of high-quality variants and associated coverage data. This data will serve as the main, importable content for the tertiary stage of analysis where variants are interpreted and classified for their impact on a patients’ disorder. We… Read more »

Automating Clinical Workflows: Part III

In the previous two articles, we explored the different steps of a clinical workflow. The first post covered the automated analysis that creates a VarSeq project. While the second post covered the interpretation steps and generation of a clinical report. These posts illustrated the ease with which these complex tasks can be carried out. Today we’ll dig a little bit… Read more »