The Benchtop tool allows you to compare two files against each other to evaluate their level of agreement and areas of difference at the individual-result level.
Any comparison in Benchtop begins with a set of two files, defined as the Baseline and Test file. Typically, these two files will be used for:
Comparing pipeline outputs against a truth set, where the truth set is the Baseline and the pipeline output file is the Test file
Comparing outputs from two different versions of a pipeline (e.g. before release or with each code change), where the v1 outputs are the Baseline and v2 outputs are the Test
Comparing outputs from two different pipelines - for example when benchmarking variant callers or performing analysis for tool selection
Comparing outputs on biological or technical replicates
Comparing Like and Non-Like Files
When comparing files in Benchtop, everything is done "apples to apples". Therefore, if you have two different file formats (for example, from two different tools), they can still be compared as long as they have fields that match to one another.
The subset of overlapping fields that uniquely identify matching records are called match keys. If you are using common generic filetypes such as CSV, TSV, and TXT, you will be prompted to set your match keys upon your initial comparison -- and if you are using built-in or custom parsers, they will be preset. You can also set or modify match keys for a given dataset at any time using the File Configuration panel.
Selecting Files for Comparison
To create a new comparison report from your workspace files, simply drag and drop the files from the Tiles view:
or use the toggle buttons in the List view:
Configuring Parsers
Selecting the appropriate file parser is key to getting the most value out of a Benchtop comparison. For most flat files (TSV/CSV/TXT) and common genomic file formats, an appropriate parser will automatically be selected for you based on the file extension.
However, more complex flat files may require custom parsing logic. To generate a custom parser, use the File Wizard. Both the File Wizard and the Parser Selector are accessible in three ways:
From the File List View
The second column of the File List view shows the selected (including pre-selected) parsers for each file. To modify the parser for a file, click on the parser name or plus sign (if no parser is selected) in the corresponding row.
From the Comparison Files Panel
Files that are already dropped into the Comparison Files drop-boxes can be configured by clicking the Configure button below the file.
From the File Configuration Panel
Access the file configuration panel from any tab under Workspace Files by clicking the ⚙️icon next to the Search bar.
Changes made in File Configuration will apply to the currently active baseline file.
Removing and Swapping Comparison Files
You may find yourself wanting to perform the same comparisons on multiple pairs of samples. To do that, simply remove the currently used files from the Baseline and Test drop-boxes by clicking the X Remove button, and replace them by dragging and dropping a new file from the Workspace Files.