GUIvariants

GUI – variant analysis

The GUI provides interactive access to some tools for variant analysis.

To perform variant calling on an alignment file, select the bam file in the left-hand panel, right-click, and select Call Variants... in the pop-up menu. This brings up a new window showing all the relevant options. Here, choose from the existing configurations or create a new configuration to perform customized calling.

To perform filtering on an existing set of variant calls, select the vcf file in the left-hand panel, right-click, and select Filter Variants... in the pop-up menu. This brings up another window where filtering criteria can be specified.

In either variant-calling or variant-filtering, pressing Ok instructs the program to commence the relevant action. Progress can be tracked in tabs that appear in the right-hand side of the main GUI window. Once the actions are complete, the output vcf files should appear in the file-manager panels on the left-hand side of the main window.