1. OverviewΒΆ

This tutorial will start with an existing project. A lot of the functionality described in this tutorial can be performed with a “Viewer” license, for those options not allowed you will get instead a warning from the software. We recommend going through the tutorial with an active license or a demo license to experience full functionality within this project. Additionally, this project could be used as a basis for further exploration, annotation and filtering. The end result will be exported data with a candidate variant.

VarSeq software supports several variant filtering workflows such as trio, cancer, and gene panel workflows to name a few. This tutorial will focus on a Cardiomyopathy gene panel workflow that utilizes a set of filtering criteria to find a clinically relevant pathogenic variant.

The ZIP file can be downloaded and the contents can be extracted to a convenient location. Then from VarSeq go to File > Open Project to select the saved project file. Alternatively, if you would like to go through the import process, see the import instructions below.

To import the original VCF files that were used in the supplied project, download them from our Data Repository through VarSeq by opening the software and going to Tools > Manage Data Sources and selecting the NextSeq 500 TruSight Cardio file from the Example Samples > NextSeq 500 TruSight Cardio folder. Select the**NA12877-Rep1_S1 and** NA12878-Rep1_S1 Variant Map files. Then click Download in the lower left corner. See Figure 1-1.

Download VCF

Figure 1-1: Download the VCF file that was in the sample process to import manually into a new VarSeq project

Return to VarSeq and select Create New Project. At this point you can either choose to use a template or start an empty project from scratch. Provide a name for the project and click Ok. See Figure 1-2.

Create a Project

Figure 1-2: Create a new project in VarSeq

Next we will import the VCF files by clicking Import Variants. Then, open the folder containing the NA12877-Rep1_S1 and NA12878-Rep1_S1 VCF files that were downloaded and click and drag the files into the import window. Alternatively, you can click Add Files and navigate to the folder with the samples and add them this way. See Figure 1-3. Click next. Now specify the sample relationships. Click next twice more and click Finished to complete the import.

Import Variant

Figure 1-3: Add VCF files to VarSeq by clicking and dragging the files into the importer or add the files through the Add Files option

A typical hereditary workflow would begin with a genetic test for patients with inherited cardiovascular disorders, hereditary cancers, or other inherited diseases that are identified through the patient’s family history and clinical presentation. Once variants have been called by a secondary analysis pipeline, the variants should be first filtered on quality of the call. Also, it is important to capture rare variants that are not found at high frequency across the general population and this can be achieved by utilizing variant frequency databases. The workflow wraps up by choosing variants that are associated with the phenotype of the patient and selecting for those variants that are pathogenic or likely pathogenic.

The second chapter or section of this tutorial will cover the Filter View, including the input and output of the filter chain, how to expand and collapse a card, how to move a card, change a card and click on a card to get a filter level report.

The third chapter will cover the Table View, including how to hide and show columns, cloning a table and linking and unlinking it to a filter result, viewing intermediate results in the filter chain, and getting column reports and histograms.

The fourth chapter will cover exporting results from VarSeq into various formats.

The last chapter will wrap up the tutorial as well as include links for where to go next to learn more about VarSeq.