4.5.2. 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, Sorted in Ascending Order by Conditions, an Active Numeric Search Filter for the Variant Allele Frequency (VAF) Column and Variant Sets Selected for Additional Analysis

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 (ie 6:75797330)

• String Columns: These columns contain strings. Cells in string columns can also contain lists of strings (ie Bethlem myopathy 2;Ullrich congenital muscular dystrophy 20 in a Conditions column).

• Categorical Columns: These columns contain categorical (ie Missense in a Classification column) 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) (ie 0.484211 in a Variant Allele Frequency) 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.

Right-clicking on a Column’s Header Displays a Menu of Options.

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. 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.

• 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.

• Query Column Values: This option identifies variants that have a value in the selected column matching the search filter requirements. Most columns in a table can be used to create a search entry with the exception of the genomic position column and any categorical fields.

  Using this feature is a convenient way to further restrict variants in a table. Once a search has been created, it can be turned on and off using the checkbox to the left of search criteria.

  Searches can be modified by clicking on the down arrow to the right. 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.

  Any active search is colored green. If it is unchecked, it will turn gray to indicate that it is inactive. If an expression is invalid, it will be orange. This option is available for String, and Numeric column types only.

• Add To Filter Chain: Adds a Filter Card to the Filter Chain to partition the variants in the table by the values in the column. See see Filter View.

• Rename: Opens the Rename Field dialog where you can enter and save a new name for a column.

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.

Right-clicking on a Column Group’s Header Displays a Menu of Options including Hiding/Showing Individual Columns in the Group.

Icons on the Table Tool Bar

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 open the Change Column Visibility dialogue where you can change toggle the check boxes to hide or show different source groups and columns.

• 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.

• Add Annotation to Window: Opens the Data Source Library dialogue allowing you to add addition annotations directly to the table. See Annotations.

• 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 Record Sets 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 the checkbox. The current filter based on the filter view is colored green. If this is toggled it will turn gray to indicate that it is inactive.

Record Sets

To create a Record Set click on the Record Set icon in the table view toolbar and select Create [Record Type] Set (ie Create Variant Set). This will open the Create [Record Type] Set dialog where you can enter in a name, initials (abbreviation), choose a color and set the sample option.

The Create a Variant Set Dialog

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 [Record Type]: Clear all records from the selected record set.

• Edit: Edit the properties of the selected record set.

• Delete: Delete the selected record set.

Detail View

The Details 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 icons in the top right of the Details View allow you to Undock and Close the view.

Docked Table Details for a Variant

In the undocked position, click “More” to show full detail about the selected cell, or click “Less” to show less details.

Undocked Details View for a Column

Copy

Information can be copied out of the Details View by selecting it and using the right-clicking to access the Copy function.