Viewing Results

Each OpenCRAVAT job produces a SQLite database containing the complete annotation results. This database is placed in the same directory as the input file and named {input_file_name}.sqlite (the name and location will differ if the job was run with the -n or -d flags).

Results can be explored in two ways: the interactive web viewer, and downloadable report files.

Generating Report Files

Report files in formats such as Excel, TSV, and VCF can be generated from a completed job using the oc report command:

oc report job.sqlite -t excel tsv

See OpenCRAVAT reports for available formats, options, and how to install additional reporters.

Interactive Viewer

The interactive viewer is used to explore the CRAVAT results using filters, tables, and visualizations. It is launched by passing a job result database to oc gui.

oc gui job.sqlite

By default the database is placed in the same directory as the input file, and is named by appending .sqlite to the end of the input file name. This will change if OpenCRAVAT is run with the -n or -d flags.

The above command will start a local python server and open a webpage using your default browser. The webpage is the interactive viewer. It is organized by tabs, shown at the top of the screen. The tabs are similar to the excel report sheets and text report sections.

Summary Tab

The Summary tab shows overall information about the job, and can be used to create, save, and load filters.

The Summary tab may also contain graphical summary widgets, which provide a high level overview of the job. Only the summary widgets installed are displayed. CRAVAT includes some widgets by default, and more can be found in the CRAVAT store. Some widgets depend on specific annotators. Widgets on the Summary tab can be resized, hidden and rearranged similarly to the widgets in the variant tab, which is explained below.

Filter tab

OpenCRAVAT filters can be applied to any annotation and affect the results displayed across the entire viewer. When the filter is changed, the data passed to every other tab, table, or widget is only the data which passes the filter.

To add filters, select the filter menu from the top bar. Individual filters are created using the drop-down menu in the Variant Filters box. As filters are created and adjusted, the number of variants passing the filter is shown below. When the update button is pressed, the viewer loads the variants and genes which passed the filters.

Filters can also be saved so that they are available across viewer sessions. Click the save button near the top of the filter menu to give a filter set a name, and save it to the sqlite database. Then the filter can be reloaded by clicking the load button, and entering the name of the saved filter. Multiple filter sets may be saved and loaded.

Variant Tab

The Variant tab is one of the main data display tabs in CRAVAT. It is divided into two sections, a data table, and a collection of visualization widgets.

For each variant, we select a representative transcript isoform using EMBL-EBI MANE. Splice variants are defined as variants within two base pairs of an exon-exon junction.

The data table shows all of the annotations available, grouped by annotator. Columns may be resized, and moved individually or as a group. Move columns/groups by clicking and dragging their header. Columns can also be removed or added to the table using the layout drop-down menu in the top left of the page.

The visualization widgets section displays a visual summary of the current row in the data table. It is designed so that the user can quickly move through the data table and understand the contents of a row at a glance.

Widgets can be manipulated in different ways. They can be resized and moved using the mouse. Widgets can be hidden by either clicking on the x button, or by using the layout menu in the top left. Hidden widgets can also be displayed again using the layout menu. Layouts can be saved and loaded to preserve certain views, or to create a check-point before making major layout changes.

Saving a layout will save the columns displayed, column order, widgets displayed, widget size, and widget order. Like filters, saved layouts are available across viewer sessions.

Gene Tab

The Gene tab is identical to the variant tab, but displays gene level information.