Table View

The Table View contains a list of variants and variant information from either the original VCF file or from data sources used to annotate the variants. The columns of data are grouped by source and by sample, if sample information was included in the original VCF file.

A table of variants with a filter chain, an active numeric search filter for the Read Depth (DP) column as well as an inactive string search filter for the Gene Names annotation column.

General Table Actions

Row Selection

To select (highlight) a row click anywhere in the row or in the box to the left of the row.

To select multiple rows at the same time, hold down the Shift key on your keyboard and select the rows or range of rows. You can also hold down Ctrl to toggle the selection of individual rows.

Resize a Column

To resize a column, hover over the edge of the Column header until the mouse changes to a resize pointer and click and drag to the desired size.

Column Types

• Chr:Pos Column: The genomic location for the variant describes the chromosome and start position of the variant.
• String Columns: These columns contain strings. Cells in string columns can also contain lists of strings.
• Categorical Columns: These columns contain categorical or an enumerated list. Cells in a categorical column can also contain lists of categories.
• Numeric Columns: These columns contain numeric values including integers, real-valued numbers (floats and doubles) as well as boolean (true or false being treated as 1 and 0 in numeric contexts such as plotting). Cells in a numeric column can also contain lists of numeric values.

Column Menu Options

To access column menus, right-click on a column header. Column menu options depend on the column type. These menus are described below. Information about a column can be obtained by left-clicking and hovering on the column header. The information will be displayed in the Detail View.

Column menu options include:

• Sort Ascending: Sort the table on the selected column in ascending order. Missing strings or values ”?” for the particular column will be placed at the top of the table when sorted in ascending order. This option is available for all column types.
• Sort Descending: Sort the table on the selected column in descending order. Missing strings or values ”?” for the particular column will be placed at the bottom of the table when sorted in descending order. This option is available for all column types.
• Hide: This option hides the selected column in the table. This option is available for all column types.
• Add to Filter Chain: Adds a filter card to the bottom of the filter chain for the column, see Filter View for more information on these filter options. This option is available for all column types.
• Group by <Column Name>: This option creates a second table that has a column of the strings on the left and all the variants in each group on the right. It is not recommended that this option be used on string columns that have a large number of unique strings. An example of a column this can be used on is to group variants by gene. This option is available only for String column types.
• Query Column Values: Identifies variants that have a value in the selected column that matches the search filter requirements. See Searching the Table for more information. This option is available for String, and Numeric column types only.
• Plot: This option creates a GenomeBrowse value plot of the non-missing values in the column. See GenomeBrowse View for more information. This option is available for Numeric column types only.

Column Groups

Columns are grouped together by either the sample identifier, the annotation source or computation algorithm. Some annotation algorithms will create more than one column group.

Right clicking on a sample level group header allows you to change which samples are displayed in the table. Right clicking on an annotation or algorithm source header, allows you to hide, delete, re-run the annotation or algorithm, and select edit column visibility for the group.

Resizing the column group will proportionally resize the columns within it.

Icons on the Tool Bar for a Table

There are several icons providing access to menus and utilities on the table toolbar. These menus and options (from left to right) are described below.

• Table Type Selection: Select the type of data to view in the table. The types available depend on the algorithms and data sources but include by default:

  • Variants
  • Samples

  Additional table types include:

  • Variants by Coverage Regions
  • Coverage Regions
  • Variants by Genes
  • Variants by <Table Name>
  • Genes

• Clone Table: Click on the duplicated spreadsheet icon to create a clone or copy of the table and place it in a new tab.

• Hide/Show: Click on the eyeball icon to change the visibility of source groups and columns. Toggling the check boxes will allow hiding or showing different fields.

• Sample Selection Menu: The outlined sample icon can be used to change how the sample level fields are collated as well as which samples are visible in the table.

  • Sample Collate: Group or collate all sample level fields by sample. This means you will have all of the fields for the first sample then all of the fields for the second sample, etc.
  • Field Collate: Group or collate all of the sample level fields by field. This means you will have all of the samples for the first field then all of the samples for the second field, etc.
  • No Samples: Hide all samples from the table view.
  • All Samples: Show all samples in the table.
  • Affected Samples: Show only samples in the table that have an Affected status.
  • Current Sample: Show only the current sample.

  For family data additional sample selection options include:

  • Current + Parents: Show only the current sample and the sample’s parents.
  • Current + Parents + Siblings: Show only the current sample, the parents and any siblings.

  For Tumor/Normal samples additional sample selection options include:

  • Tumor: Show only samples that are specified as tumor samples.
  • Tumor + Normal: Show tumor/normal pair samples.

• Record Sets: Record Sets allow you to create a persistent selection of records (variants, samples, etc.) for either the current sample or project. See Record Sets for more information.

• Hide/Show Details Window: The Hide/Show icon can be used to dock and undock the details pane. In the docked position, the details pane is docked to the right of the table. In the undocked position, the details pane can be accessed by clicking on and hovering over any cell in the table view. See Detail View for more information.

• Table Filters: This linking filter provides options for how a table interacts with a filter chain. Toggle the filter and the lock in the filter to change the behavior. See Table Filters for more information.

• Sort Filter: If you have your table view sorted in either ascending or descending order by any of the columns, the sort filter will be displayed next. The sort filter will have the same name as the column that was used to sort the table, along with an embedded icon indicating the direction of the sort (ascending, or descending). The direction of the sort can be changed by toggling the embedded sort direction icon. The sort filter can be removed by clicking on the X icon within the sort filter.

• Search Filters: A search filter may be displayed next. The searches will by default have the same name as the column used to populate the table. The filters can be activated/inactivated by clicking on them to toggle their state. See Searching the Table for more information.

Table Filters

Table filters provide linking options for how a table interacts with a filter chain. Once a filter has been created it can be turned on and off by clicking on it to toggle the color. The current filter based on the filter view is colored blue. If this is toggled it will turn gray to indicate that it is inactive.

Searching the Table

Searching the table is a convenient way to further restrict variants in a table. Once a search has been created it can be turned on and off by clicking on it to toggle the color. Any active search entry based on a table column is colored green. If this is toggled it will turn gray to indicate that it is inactive. Most fields in the table can be used to create a search entry with the exception of the genomic position column and any categorical fields.

Search entries can be modified by double clicking on them. Numeric searching provides options for basic operators == (equal to), <=, >=, <,>, and a numeric value can be added after the operator. Boolean searching provides ==True and ==False options.

String searching provides options including:

• startswith: starts with the specified string
• endswith: ends with the specified string
• contains: contains the specified string

String searching will always be case insensitive.

If an expression is invalid it will be orange. If an expression is valid and active it will be green.

Record Sets

To create a Record Set click on the Record Set icon in the table view toolbar and select Create [Record Type] Set (e.g. Create Variant Set).

This will open the Create [Record Type] Set dialog. See To create a variant set enter in a name, initials (abbreviation), choose a color and set the sample option.

To create a variant set enter in a name, initials (abbreviation), choose a color and set the sample option

Once a record set is created records can be added to the set by individually clicking on the box in the row for the record or by using options in the record set sub-menus.

To view the options for a record set, open up the Record Sets menu and click on an existing record set. The options include:

• Set to Current [Record Type]: Sets the flag for the selected record set for all records currently in the table view.
• Add to Current [Record Type]: Add all of the records in the table view to the existing records in the selected record set.
• Clear: Clear all records from the selected record set.
• Edit [Record Set Name]: Edit the properties of the selected record set.
• Delete [Record Set Name]: Delete the selected record set.

Detail View

The detail view displays detailed information on variants, data sources and algorithms. Clicking on a variant in the table, a column header or a column group header will update the information in the detail view.

The detail view can be in a docked or an undocked position.

In the docked position, the detail view is displayed to the right of the table. In this position the full details of a cell are displayed. To undock the detail view, click on the square undock button in the detail view header.

Docked Table Details for Column

In the undocked position, the detail view can be accessed by clicking and hovering over a cell in the table. The detail view then opens up near the mouse click.

Undocked Table Details for Column

Copy

Information can be copied out of the detail view by selecting it and using the Copy button at the upper right corner of the view. History

More/Less

In the undocked position, you click “More” to show full detail about the particular cell that was clicked on, or click “Less” to show less details.