Automatically clear existing samples when new samples are added

When you open a sample in IGV, if other samples are also being displayed, then leave this option cleared to view all samples; otherwise, select it to clear all other samples from the display other than the currently loaded sample.

Also load variants’ samples

Selected by default. When viewing a variant in IGV, if you have selected this option, then the sample information for the variant, such as coverage distribution, read pile-up, is also loaded and viewable in IGV.

Automatically search and load missing bam files

If you did not import a BAM file for a sample, then to view the BAM file in IGV, select this option. Geneticist Assistant then looks for the BAM file that matches the VCF file name either in the VCF directory/sub-directory or, if applicable, in the NextGENe project file directory/sub-directory.