https://sourceforge.net/p/bamformatics/wiki/GUIvariants/Recent changes to GUIvariantsenWed, 06 Mar 2013 21:37:48 -0000https://sourceforge.net/p/bamformatics/wiki/GUIvariants/<div class="markdown_content"><h2 id="gui-variant-analysis">GUI – variant analysis</h2> <p>The GUI provides interactive access to some tools for variant analysis.</p> <p>To perform variant calling on an alignment file, select the <em>bam</em> file in the left-hand panel, right-click, and select <em>Call Variants...</em> 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. </p> <p>To perform filtering on an existing set of variant calls, select the <em>vcf</em> file in the left-hand panel, right-click, and select <em>Filter Variants...</em> in the pop-up menu. This brings up another window where filtering criteria can be specified. </p> <p>In either variant-calling or variant-filtering, pressing <em>Ok</em> 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.</p> <p><br /></p></div>TomaszWed, 06 Mar 2013 21:37:48 -0000https://sourceforge.netb3f158cc73d51a89b1bb192fcfd96cc78eb1965e