VCF Benchmarking app

Overview

The VCF Benchmarking app allows you to interactively view SQLite files which are generated by running the VCF Benchmarking workflow. Note that you need to run the VCF Benchmarking workflow to generate SQLite files prior to using the VCF Benchmarking app.

This functionality should not be confused with VCF Benchmarking workflow, which is used for benchmarking variant calls. After obtaining benchmarking results with the VCF Benchmarking workflow, use this app to analyze those results.

Analyze an SQLite database file

1. Navigate to your project which contains the SQLite files.
2. Click Interactive Analysis.

3. Click Open within the VCF Benchmarking section (note: the number of available files will be shown).
4. Click Add files.
5. Only the output files of the previously ran VCF Benchmarking workflow will be displayed.
6. Select a file (or multiple files if you want to compare them, see below).
7. Click Select. The VCF Benchmarking app will be shown.

The following filtering options are available:

• Region Stratification - filters variant stratifications by region
• Character Stratification - filters character stratification by type.
• Filters applied - specifies how to treat variants that have a non-passing filter value
  • All - choose apply all filters, i.e. variants with non-passing filter values are excluded.
  • None - choose to ignore all filters i.e. variants with non-passing filter values are included in the calculation.

Compare multiple SQLite files

To compare multiple SQLite files follow the same procedure as described above and select more than file. The comparison of multiple files is shown.

Click a file in the list and the Venn diagram as well as the SNP variants and INDEL variants (denoted with blue color) will show information related to that file.

Further options

• Collaborate - share what you see in the VCF Benchmarking app with your collaborators by sharing the page's URL.
• Select different files - use Change selection on the right to select a different set of files.
• Change the sort order - click the F (filtered results) or W (unfiltered results) columns to set the desired sort order for the results.
• Change the sort order - click F to sort by filtered results or W to sort by unfiltered results.
• Enable or disable the heatmap - use the toggle above the table to enable or disable the heatmap.
• Blue columns contain filtered results while green columns contain unfiltered results.
• Column shading indicates the number of available results, with more results represented by a darker shade.
• Exclude a file - click X next to a file to exclude it from the comparison.
• Switch Interactive Analysis apps - Click the icon to switch apps.