As our regular customers may know, we write our blogs to provide relevant content to any NGS-based analysis with VarSeq. Our goal here at Golden Helix is to provide top quality software and guidance on how to use the software efficiently to perform variant analysis. However, this blog series will take a more general perspective and supply some insight into optimizing a full high throughput bioinformatics pipeline from FASTQ to clinical report. Our full software stack not only produces top quality variant calling and interpretation with our secondary and tertiary capabilities but also provides the means of storing your complete set of genomic data in VSWarehouse. Users can then leverage this collection of stored data against future samples to isolate rare variants, as well as standardize the capture and accessibility of final variant classifications and clinical reports.
To make for a more efficient read, this blog will be split up into a series covering the following topics:
- Part 1. Secondary Analysis with Sentieon: Rapid and Accurate Variant Calling
- Part 2. VSPipeline: Automating your Tertiary Workflows
- Part 3. VarSeq: Interpreting the Results
- Part 4. Warehouse: Genomic Data Storage and Project Management
To navigate through these steps in a simple yet relatable fashion, we will call variants through a targeted gene panel using Sentieon. The output VCF and BAM files will be automatically processed through a predeveloped project template via a VSPipeline batch script. Next will be the variant interpretation deep-dive via ACMG guidelines in VarSeq’s VSClinical interpretation hub with the production of a comprehensive clinical report. Then lastly, we will capture the variant classification and all other relevant data into VSWarehouse to leverage the stored knowledge for future projects and to track evolving clinical evidence over time.
The purpose of the blog will be to expose users faced with high sample loads to the full-stack capabilities Golden Helix provides. We understand the need for rapid but accurate solutions for all the above steps and we have worked diligently to maintain these standards when developing our software solutions.
