Explore Variants and Structural Variations

The Variants view consists of a table with a row for each variant position. This view can be generated for any combination of supported data types; see the section below the table for details. The Variants view is synchronized with the Analysis view and with Alignment tracks in that view. Click on any Variants view row to locate the variant in the Analysis view.

The Variants view comes in two versions (single-sample and multi-sample) and can be generated with or without filters applied. In addition, a selected subset of variants can be placed in a “set,” which can be viewed as a separate multi-sample Variants view.

These different versions of the Variants view, along with the Structural Variations view, can appear very similar at first glance. The following table describes how to recognize each type of view.

View type	View tab	Tool set in view header	Notes
Multi-Sample Variants	Text always reads “Variants”	No filter applied: Filter applied:	This type of table was first released in GenVision Pro 18.0 and is similar to the SNP table in ArrayStar. The icon features a green bar. This version includes columns associated with the human Variant Annotation Database (VAD) Many more Variants menu commands are available when this version of the view is active compared to the single-sample version of the view.
Single-Sample Variants			This version of the view is included in all versions of GenVision Pro and is similar to the Variants table in SeqMan Ultra. Text on view tab uses the current sample Name from the Experiments section of the Explorer panel. The icon features a blue bar. The filter tool icon does not change after filter is applied.
Structural Variation	Text uses sample name:		This version of the view is included in all versions of GenVision Pro and is similar to the Contig Structural Variations table in SeqMan Ultra. Text on view tab uses the current sample Name from the Experiments section of the Explorer panel. The filter tool icon does not change after filter is applied.
Variants Set			A variants set is essentially a multi-sample Variants view showing only the selected variant rows. Text on view tab uses the current set Name from the Variant Sets section of the Explorer panel.

Combining data types to create a variants table:

GenVision Pro lets you import any combination of SeqMan NGen assemblies, BAM, VCF, and GFF files to a new session or to an existing session that already contains data. This means you can add, remove, and compare variant analysis data sets from different sources and at different points in the data analysis pipeline. For example, you could import BAM files from a third party pipeline; variants are called automatically during import. Then you could compare those variant calls to imported VCF files and SeqMan NGen assemblies.

When creating a variant table note that the same reference genome must be used for all data sets. GenVision Pro will warn you if mismatched references are detected. Also note that each time a new variant data set is added, the variant database is recalculated. This may take a long time if you are working with large data sets.