1. OverviewΒΆ

VarSeq software supports both trio and gene panel variant filtering workflows. This tutorial focuses on a trio workflow to find candidate de Novo variants to highlight and demonstrate ways that the filter chain can be used.

A typical family trio workflow can be summarized in Figure 1-1. Once the variants have been called by a secondary analysis pipeline for each member of the trio (either simultaneously or individually) the variants should be filtered based on the quality of the calls. A typical goal of trio analysis is to identify rare putative mutations. To identify rare mutations, variant frequency databases can be used to remove variants that are present at high frequencies among large population groups. Finally, specific inheritance patterns can be used to identify variants meeting that mode of inheritance’s criteria. What is left is a list of candidate variants.

Trio Workflow

Figure 1-1: Simplified Trio Analysis Workflow

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. If you have an active license or demo license all functionality will be available and this project can be used as a basis for further exploration, annotation and filtering.

The end result will be exported data with a short list of candidate variants.

After the ZIP file has been downloaded, extract the contents to a convenient location. Then from VarSeq go to File > Open Project to select the saved project file. See Figure 1-2.

VarSeq Map and Chapters

Figure 1-2: Different views of VarSeq labeled for the de Novo project

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, change sample visibility, collate by field, and plot a column.

The fourth chapter will cover the interaction between the filter and table views, including 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 fifth 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.

Note

The original VCF file that was used to import the data into the supplied project can be download from our Data Repository through VarSeq by going to Tools > Manage Data Sources and selecting the YRI_Exome_Filtered3.vcf.gz file from the Example Samples > YRI Trio - 1000Genomes Phase3 folder and clicking Download in the lower left corner.