2. The Filter View InterfaceΒΆ

Highlighted Filter View

Figure 2-1: The VarSeq window with the filter view highlighted and detailed

  1. First, we will examine the input and output number of variants in the filter chain. You should see a number at the top right of the filter chain (as noted in Figure 2-1) that indicates how many variants were imported from the VCF file for the current sample. This number should be 50,691. See also Figure 2-2.

    Input Variants

    Figure 2-2: The number of variants from the VCF file for the current sample (Affected Child)

    You should also see a number at the bottom right of the filter chain (as noted in Figure 2-1) that indicates how many variants remained for the current sample after applying the current filter chain and all enabled filters. This number should be 36. See also Figure 2-3.

    Output Variants

    Figure 2-3: The number of variants from the VCF file for the current sample (Affected Child) after applying all of the filters in the filter chain

    Note

    Two filters are currently not enabled. These filters are grayed out and all of the variants pass through these cards (the card has no effect on the variants in the filter chain).

    You should also notice a number on each filter card enabled or otherwise. This is the number of variants that remain in the filter chain after applying the particular filter.

  2. Next, we will examine a filter in more detail. In the current project, the filters are shown in a collapsed state. These filters can be examined by expanding the cards and showing the filter criteria. Click on the open rectangle (see Figure 2-4) for the Read Depths (DP) (Current) card.

    Expand Icon for RD Card

    Figure 2-4: Click on the open square for the Read Depths (DP) (Current) card to expand the card and see the filtering criteria

    This filter is a numeric filter which means there is a numeric threshold box and options on how to filter based on that threshold. Currently only variants for the current sample are kept if the read depth is greater than 10 reads. See Figure 2-5.

    Expanded Numeric Card

    Figure 2-5: 1,378 variants had a read depth of less than 10. The number of variants with a read depth score equal to 10 was 301, while 49,008 variants had a read depth of greater than 10. Four variants were recorded as missing for the current sample.

  3. To see what happens to the filter chain when changing a numeric filter, change the value of 10 to 50. You should see that only 16,926 variants pass this filter and only 28 remain after the full filter chain. See Figure 2-6.

    Changed RD Threshold

    Figure 2-6: Changed the read depth threshold from 10 to 50 which resulted in the filter chain updating the resulting variants

    Now, change the threshold back to 10 and collapse the card by clicking on the horizontal line in the upper right corner of the card. See Figure 2-7.

    Collapse Read Depth Card

    Figure 2-7: Collapse the Read Depth card to hide the threshold and criteria information to conserve space

  4. To change the order of the filtering operations, click on a card and drag it to the desired location. We will demonstrate this by moving the Effect (Combined) card that is in the Candidate Variants filter container to the top of the filter chain. To do this first click the open square at the top of the filter container for Candidate Variants. See Figure 2-8.

    Expand Filter Container

    Figure 2-8: Expand Candidate Variants Filter Container to show

    Then, click on the Effect (Combined) filter card and drag and hover over the top of the filter chain until the black horizontal I-bar appears over the Read Depths (DP) (Current) card. See Figure 2-9.

    Move Filter Card

    Figure 2-9: Move the Effect (Combined) filter to the top of the filter chain

    For this particular filter chain this operation does not affect the final result but it does affect the intermediate results.

  5. Now expand the Effect (Combined) Card. See Figure 2-10.

    Effect (Combined) Expanded

    Figure 2-10: Effect (Combined) card expanded to show the categories possible for variants with this filter

    A filter card can be created from any column in the variant table. When you click on any column header in the variant table, the Details view will update to reflect the information from the source as well as provide a table of the values contained within the column and the proportion of values seen for the input set of variants for each category.

    For example, you may wonder which column the ‘Effect’ filter card is from and what each category (LOF, Missense, Other, and Missing) represents. By clicking on the ‘Effect’ column header in the Variant Table view, the Details View will update with additional information from this source. See Figure 2-11.

    Effect Details

    Figure 2-11: The Details View for the Effect (Combined) filter card

  6. Now, collapse the Effect (Combined) card and move it back to just above the Clinical Significance card in the Candidate Variants filter container. Next, expand the African American MAF card and click on the yellow histogram icon. This will give a histogram of the minor allele frequencies for input variants for this card. Figure 2-12.

    Histogram of AAF

    Figure 2-12: The histogram of the African American MAF (NHLBI) values for the variants input in to the filter