5. Exporting ResultsΒΆ

  1. For this chapter, the definition of “export” will be loosely interpreted. The first “export” we are going to perform is exporting a ClinVar RCV number to the ClinVar website to examine a variant in further detail.

    First, we will narrow down the list of variants to just two candidate de Novo mutations with ClinVar ID’s. To do this, right-click on the Clinical Significance card and select Enabled. See Figure 5-1.

    Enabled Clinical Significance

    Figure 5-1: Right-click on the Clinical Significance filter card and click on Enabled to activate this filter

    The bottom table (final filter chain result table) should update to just two variants. Scroll over to the ClinVar column group. See Figure 5-2.

    ClinVar Results

    Figure 5-2: The ClinVar information for the three clinically significant variants

    Double-click on the RCV number for the bottom variant. This will launch a web browser displaying results from ClinVar for this variant. See Figure 5-3.

    ClinVar Web Browser

    Figure 5-3: The variant in the ClinVar website in an internal web browser

  2. Rows can also be copied out of the table individually. To do this, right-click anywhere in a row and select one of the options. Information from a cell can also be copied out of the table from the right-click menu as well. See Figure 5-4.

    Export a row or cell

    Figure 5-4: Copy information from a row or a cell to the clipboard for pasting in or out of the program

  3. To copy information out of the Detail View, you can either click on the Copy button on the lower right corner of the view to copy all of the visible information or you can click and drag to make a selection and either use Ctrl + C or right-click and select Copy to copy the information and formatting to the clipboard. See Figure 5-5.

    Copy Details to Clipboard

    Figure 5-5: Copying information out of the detail view preserves any HTML formatting

  4. The variants and annotation information from the table can also be exported directly to different file formats including VCF, Microsoft Excel XLSX, and text (TXT).

    Click on the Export icon on the top left of the VarSeq Window and then select VCF File.... See Figure 5-6.

    Select VCF Export

    Figure 5-6: Click on the Export icon and select Export to VCF

    Select the Variants: Trio de Novo Workflow: NA19240 table to be exported in VCF format then click OK. See Figure 5-7.

    Select Table to Export

    Figure 5-7: Exporting single table to VCF

    All of the annotation information can be exported in the VCF file, which will include all samples. Just as columns and column groups can be hidden and shown, the available columns and column groups can be selected for inclusion in the VCF file.

    Leave all default options, click on Browse to select a location to save the file to and set the file to export to export_de_novo_VarSeq_tutorial_data - {{sample}}.vcf.gz or another name of your choice. Once the options are set click Export. See Figure 5-8.

    Export Table to VCF

    Figure 5-8: Select fields and specify file name and path to export the data to a VCF file

    This file can then be imported into any other program that takes VCF files or reimported into VarSeq for accounts that have an active license.