4. Updating Tables from Filter Input and Intermediate ResultsΒΆ

  1. Tables can either update when filters results are clicked on or they can be fixed to a particular filter result. To tell if a table is locked to a particular filter, examine the table filter icon. If the padlock icon is open the table is unlocked. If it is closed then it is locked to the particular result identified in the icon. See Figure 4-1.

    Table Not Locked

    Figure 4-1: The current table shows the results of the Clinical Significance filter but it is not locked.

    Click on the final result of the filter chain. The table filter icon should now say “Trio de Novo Workflow”. We want to keep a copy of this table and create another table to explore intermediate results. So click the lock icon to lock the current table then click the clone icon in the Table View tool bar. This will lock the current table and create a copy. See Figure 4-2.

    Clone Table

    Figure 4-2: Clone the current table to lock it to the filter chain results and create another unlocked table

  2. Click the tab for the copy to bring it to the front and unlock the filter view then click on the filter results for the de Novo Candidate filter container. You should see the top table update to include all 97 variants from that card, however, the bottom table locked to Trio de Novo Workflow does not update. See Figure 4-3.

    Intermediate Results

    Figure 4-3: Clicking on intermediate results updates the unlocked table but does not update the locked table

    Click around some more, expand some cards and see how the table updates.

  3. Click on the de Novo Candidate filter again, and expand it. This time expand the Zygosity (Current) card, and right-click on the Homozygous Variant category and select Results For Only This Expression. This will update the table to be all Homozygous variants for the current sample (the child) from the original input set of variants. See Figure 4-4.

    Only HomoVar

    Figure 4-4: Display all homozygous variants for the child from the original input set of variants

    See in Figure 4-5 how the table filter icon changes to indicate a particular category was used for the variants to display in the table. See Figure 4-5.

    Only HomoVar Table

    Figure 4-5: All homozygous variants for the child in the table view

  4. Next, click on the input variant count to display all of the original imported variants in the table view. See Figure 4-6.

    Input Variants

    Figure 4-6: Display all input variants in the table

  5. Click on the lock icon in the table to lock the top table to the input set of variants. See Figure 4-7.

    Locked to Input Variants

    Figure 4-7: Lock the table displaying all of the input variants

  6. Finally, we are going to generate column reports for a few fields. From the table, scroll over to the Effect (Combined) column in the RefSeq Genes 105v2, NCBI column group. Click on the column header to generate the column report. See Figure 4-8.

    Effect Combined Report

    Figure 4-8: The Effect (Combined) column report in the detail view.

    If you scroll over to the Details View, you can see information on the categories of this column. See Figure 4-9.

    More Effect Combined Details

    Figure 4-9: The Effect (Combined) column report scrolled down to show details on the categories in this column

    Do the same thing for the Clinical Significance category in the ClinVar column group. See Figure 4-10.

    Clinical Significance

    Figure 4-10: Clinical significance column report

    Finally, get the column report for the Variant Allele Freq column for the proband. As this is a numeric column, a numeric histogram is displayed. See Figure 4-11.

    Alt Allele Freq Details

    Figure 4-11: Alternate Allele Frequency column report for the Proband