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Filter by experiment

The Experiment screen is the first of several screens for filtering a multi-sample Variants view or set, and is where you choose the experiments and comparison baselines used to filter variants in the Variants view or in a variant set. The Experiment wizard screen is dynamic and will provide new options or hide other options depending on your selections made elsewhere on the screen.

Among other options, you can use this screen to set up a control and/or replicates and then filter based on differences between experimental samples or between these samples and a control (AKA “wild type” or “baseline”) sample.

In the Compare experiments section, GenVision Pro may have already pre-selected an option based on the samples and their names, but you can use any available option. Choose whether you want to filter experiments Individually, compare them To (one) baseline, compare them To one or more baselines, or compare exactly two experiments Pairwise. The option you choose will affect which options are available in the rest of the Experiment screen.

Choice Instructions
Individually Choose this option if you have no replicate or control samples. This option will let you filter variants that are in only one specific experiment, are in all experiments, occur at a certain frequency threshold in any experiments, and similar scenarios.

  • Make a selection from the “Include variants that pass filter and are” drop-down menu.



  • If prompted, enter a value for the Min. percent of experiments.

  • If prompted, check boxes for those experiments you wish to include. You can also use the Select All or Select None buttons.



  • If you chose Present in any selected Venn diagram regions, click or use Ctrl/Cmd+click to select the region(s) of the diagram whose variants you want to include. See the notes below this table for information about Venn-based filtering.
To baseline Choose this option if you have a control, but no replicate samples. This option identifies variants that are enriched in samples as compared to a single control. p(banner tip).

  • Select a sample from the Baseline experiment drop-down menu. The baseline experiment will then disappear from the table on this screen.

  • Make a selection from the “Include variants that pass filter and are” drop-down menu.



  • If prompted, enter a value for the Min. percent of experiments.

  • If prompted, check boxes for those experiments you wish to include. You can also use the Select All or Select None buttons.



  • If you chose Present in any selected Venn diagram regions, but not in baseline, click or use Ctrl/Cmd+click to select the region(s) of the diagram whose variants you want to include.
To one or more baselines This option identifies variants that are enriched in samples as compared to any number of controls.


  • Make a selection from the “Include variants that pass filter and are” drop-down menu.



  • If prompted, enter a value for the Min. percent of experiments.

  • In the Baseline column of the table, check boxes for those experiments you wish to use as baselines. If the sample name includes text like “wildtype,” “WT,” or “control,” GenVision Pro may automatically add checkmarks, but you can override these selections if needed. In the Selected column of the table, check boxes for the experiments you wish to compare to those baselines. Note that if you are filtering based on a Venn diagram, you must select 1-3 experiments.



  • If you chose Present in any selected Venn diagram regions, but not in baselines, click or use Ctrl/Cmd+click to select the region(s) of the diagram whose variants you want to include. If you did not select 1-3 experiments in the table, a prompt will ask you to do so, or to choose an option other than a Venn diagram.
Pairwise Choose this option to identify variants that are enriched in disease samples compared to non-diseased samples from the same subject. For instance, you can filter for variants that are present (or absent) in a tumor sample vs. a control. In this filter setup, each experimental sample has its own “normal tissue” control.

  • Make a selection from the “Include variants that pass filter and are” drop-down menu.



  • IMPORTANT: Before checking or unchecking samples in the table, first order samples as desired.

    GenVision Pro will attempt to pair samples in alternating white/gray rows based on sample names, and will attempt to place control samples at the top and without checkmarks. To override the sort order, select a row and use the up/down arrows on the right to place pair members in the order corresponding to the choice made in the drop-down menu.

  • If prompted, enter a value for the Min. percent of pairs.

  • Check boxes for the experiments you wish to include in the paired comparison. You can also use the Select All or Select None buttons.


Notes about filtering based on a Venn diagram:

The Experiment screen lets you filter based on intersections, unions, or complements of a Venn diagram of the sets. When filtering based on Venn diagrams, note that:

  • The size of Venn sets is not proportional to anything and does not indicate the size of a set.
  • You can use Cmd/Ctrl+click to select multiple areas in the diagram.
  • You can hover a mouse over any part of the diagram to see the full name of a set, rather than an abbreviation.


Once you have made your selections, do any of the following:

  • To select additional filtering options in the wizard, click Type, Impact, Alignment, or Database on the left of the wizard. If you are filtering a variant set, you can also click Name to overwrite the default name and notes for the set.
  • To apply the screen options and keep the wizard open, click Apply. Note: Once you press Apply, the button becomes temporarily disabled. When you make further changes to the filter, the button is once again enabled.
  • To apply the screen options and close the wizard, click OK.

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