Filter View

The Filter View contains one filter chain for each sample. By default only affected samples are shown in the Filter View (one sample at a time). To navigate between samples use the left and right arrow buttons on either side of the sample selection menu in the toolbar for the primary view. To switch between showing only affected samples or all samples, select Show All, Show Affected Only or Show Tumor Only in the drop down menu or in the right-click menu.

To access options for the filter chain, any filter cards or containers, click on the wrench in the upper right of any chain, container or card or right-click any where in the card.

Lock the Filter Chain

Filter chains can be locked to prevent modification. A filter chain can be locked or unlocked by clicking the padlock next to the filter chain name. Full control and modification of the filter chain is available when unlocked. Filter chains are unlocked by default. Locked filter chains are protected from accidental modification, but can be unlocked at any time.

When a project with a locked filter chain is saved as a template, the option to protect filter chain locks will be available. Enabling this option will prevent the locked filter chains in all projects created from the template from being unlocked. In a project created from a template with the filter chain lock protected, the padlock next to the filter chain name will be grayed out and disabled. It indicates that the filter chain is locked, but the lock status cannot be changed. A locked filter chain will not have many of the options listed below for modifying filter cards and the filter chain.

Edit Titles

To change the title or name of a filter chain, container or card, double click on the existing name to enter into edit mode.

Update Current Table View to Filter Results

To display the results of a filter chain, container or card in the current table choose one of the following options:

  • Results Up Through This Filter: From the menu of a filter chain, container or card, select this option to display all variants that remain in the Filter Chain after applying the current filter. This means the particular filter criteria and all previous filter criteria have been met for the variants displayed in the Table View.
  • Results For Only This Filter: From the menu of a filter chain, container or card, select this option to display all variants from the original set of variants that meet the filter criteria of only the current filter.
  • Click on any Filter Result: Clicking on any integer filter result (count of variants satisfying the applicable filter criteria) will update the Table View for the current table as long as the table is linked to the filter.

Disable or Enable Filter

To disable a filter chain, container or card, click on the check-box next to the title to remove the check mark. You can also disable a filter chain, container or card by right-clicking and from the filter menu select Enable.

If there is a check mark next to the title the filter chain, container or card or if there is a check mark next to Enable in the right-click menu the filter is enabled, otherwise it is disabled. If a filter is disabled the contents of the filter are grayed out and all variants pass through the filter chain, container or card.

Invert Filter Logic

To quickly invert the logic for a particular filter, select Inverted from the right-click filter menu. An inverted filter icon (orange exclamation mark) will appear next to the title to indicate that the filter logic has been inverted.

Configure Filter Chain or Container

A filter chain or container can contain one or more filter cards. If more than one filter card is present, the filter container can either require that the results satisfy the criteria of all contained filters or any contained filter. This is done by switching the logic operator from AND to OR or vice-versa. To change the logic of the filter container either click on the wrench icon or switch from AND to OR or vice-versa in the right-click filter menu. The options available are:

  • AND: Results satisfy criteria of all contained filters
  • OR: Results satisfy criteria of any contained filters

If a filter container logic operator is set to AND then all filter cards or containers will be vertically stacked. If the logic operator is set to OR then all filter cards or containers will be horizontally stacked.

Note

If the filter container logic operator is set to OR it is possible that variants can be counted twice in complicated filtering scenarios.

Configure Filter Card

The input of a filter card is a data source, a field and potentially a sample for per sample matrix fields. In addition, depending on the data type of the field selected, the filter card requires criteria to be set on the data. If no criteria are set, all variants pass through the filter.

To change the data source, field or sample used for the filter card, either click on the wrench icon in the upper-right of the filter card then click on the three dots ....

To change the filter criteria, expand the filter card by clicking on either the single vertical bar (OR’d filter container), single horizontal bar (AND’d filter container), or square (filter card) to access the desired filter criteria.

The number next to each criteria indicates how many variants meet that criteria. The number at the bottom right of each filter card indicates how many variants will pass through the filter based on the selected criteria.

The criteria for filter cards depends on the data type, options for each data type are below.

  • Binary: If a data field is binary (or boolean, dichotomous, etc.) there will be up to three possible categories (True, False, Missing). Click one or more criteria to indicate which variants to keep in the filter chain.
  • Numeric: This type includes integer, real-valued (float or double) fields. By default one threshold criteria will be set to 0. This can be changed by double clicking in the text box and changing the threshold to the desired value. Additional thresholds can be added by clicking on the plus icon ‘+’. To delete a threshold, click on the minus icon ‘-‘ next to the threshold. Once thresholds are specified, the criteria to determine which variants to keep can be specified by clicking on the desired criteria.
  • Categorical: If the data type is categorical then all of the possible categories are listed in the filter card. Click one or more criteria to indicate which variants to keep in the filter chain.
  • String: If the data type is a string, then enter in a string into the text box to filter on. All variant counts in this type of card are not mutually exclusive as a string can meet all criteria simultaneously if there is an exact match (all string filter card criteria are case sensitive). The possible criteria for string filtering include:
    • Matches <string>: The number of variants that have a value in the selected field that match the string exactly.
    • Starts with <string>: The number of variants that have a value in the selected field that start with the string.
    • Contains <string>: The number of variants that have a value in the selected field that contains the string.
    • Ends with <string>: The number of variants that have a value in the selected field that ends with the string.
    • Missing: The number of variants that have a missing value in the selected field. If no string is specified, the missing criteria will still be available for selection in the card.
  • Segment: This option only appears when the data selected is the Chr:Pos column. By default the filter criteria will include the entire range of chromosomes and their corresponding positions (ex. 1: 1 - X: 155,270,560) for the imported dataset. After a single range is entered results will be split into before the range, range, after the range and other categories with corresponding counts. Additional ranges can be added by clicking the plus icon ‘+’. To delete a range, click on the minus icon ‘-‘ next to the range. Once all ranges are specified, the criteria to determine which variants to keep can be specified by cliking on the desired criteria.

Add Filter

To add a filter card, from the right-click filter menu select Add Filter. This will place the filter card in the active filter container used to launch the filter menu. Once a filter card has been created, the card can be configured by clicking on the wrench icon and the three dots ... to select the source. See above.

Add Filter Container

To add a filter container, from the right-click filter menu select Add Filter Container. This will place the filter container in the active filter container used to launch the filter menu. Once a filter container has been created, the container can be configured by clicking on the wrench icon. See above.

Delete

To delete a filter container or a card, from the right-click filter menu select Delete. This will delete the selected filter card or container and any filter cards and containers contained within.

Error or Status Messages

The bottom of a filter container or card is used to display error or status messages. This includes the total variant count of variants passing through the filter. If a computation is currently running a spinner will be visible on any filter cards waiting for an algorithm to finish. If there was an error with the computation of the filter a warning icon will be visible with a short message.