Creating a New Project

How do I create a new project?

  • To create a new project, click on Create New Project.
  • Select a project template from the list of existing templates. Information about each template will be displayed on the right.
  • Verify the Genome Assembly matches the assembly used to align your data and specify a project name and location to save your project.
  • An empty template can be used to create a new workflow. This is an advanced option.

How do I use a workflow to import my data?

  • A workflow is called a project template in VarSeq. You can select a template when creating a project. This will import your data using the established workflow for filtering and annotation.

How do I add data?

  • You can import one or more variant files into a new project. VarSeq also supports annotating from numerous other file types.
  • If your project was created from a template, the Import Variants dialog will automatically appear after creating a new project. Otherwise, you can click on the Import Variants button and select one or more files to import.
  • Once the files have been selected, compressed and indexed you will be prompted to edit the sample information. You can change the sample name, affection status, and if the samples are related, set the parents for the children. Sample information can be imported from a text file. BAM files can be linked to sample data for coverage statistics. For CNV analysis associating the BAM files is required for calling CNVs.

How do I annotate my variants?

  • From the main tool bar, click on the Add Icon and select Variant Annotation…. Choose the annotation source and then click Select. All imported variants will be annotated against the selected source. See Figure 1.
Figure 1: Add Variant Annotation to a VarSeq project

How do I run an algorithm on my data?

  • From the main tool bar, click on the Add Icon and select Computed Data…. On the left is a list of possible computation algorithms. See Figure 2.
Figure 2: Add an algorithm to a VarSeq project

How do I create a filter?

  • To add a filter card for a particular column or field in a table, right-click on the column and select Add To Filter Chain .
  • The created filter will be placed at the bottom of the filter chain. This card can be moved around to any location in the chain by clicking on the card, and dragging and dropping where desired.

How do I mark variants in the table view?

  • First create a record set by clicking on the Record Sets Icon and then click on the box for the particular variant you want to mark. See Figure 3.
  • To mark all current variants in a table select Set to Current Variants in the record set’s sub-menu. See Figure 4.
  • To add all current variants in a table to an existing record set select Add Current Variants in the record set’s sub-menu. See Figure 4.
Figure 3: Creating a Variant Set
Figure 4: Adding variants to a Variant Set

How do I export data?

  • Go to File > Export or click on the export icon and select the format to export the data to. See Figure 5.
  • Select the table to export. Multiple tables can be selected for Excel XLSX export, with one table per tab in the file.
  • Select the column groups and fields to export in addition to the file options. Then select which samples to export, current only, affected only or all samples. One file will be created per sample.
  • Samples currently visible in the table will be included in the exported file.
Figure 5: Exporting data from VarSeq
Updated on February 9, 2021

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