VCF Variant Files

VCF stands for Variant Call Format, and this file format is used to encode genetic variant sites and genotypes. The file includes informatioThe format is further described at https://samtools.github.io/hts-specs/

Viewing a VCF File with Genotypes

	The section on the top displays each variant site.
	If the file also includes sample data (optional), each sample is displayed as a row of genotypes at the variant sites specified at the top. Dark blue = heterozygous, Cyan = homozygous variant, Grey = reference.

If a file has more than 10 genotypes, the VCF file will be opened in its own pane, with a scroll bar, as shown below.

VCF Popup Menu

To see the options for changing the view of your VCF file, right-click on a variant.  Some of the options are specific to the variant selected. Find more details on the menu options on the Pop-up Menu page. 

To change the genomic window size at which VCF data is loaded, right-click and select Set Feature Visibility Window...

To change the color coding of the plot, select Color By>Allele.

The Sort Variant By options allow you to sort the set by a trait of a specific variant.  You can select the sort twice for the same variant to flip it, i.e., if you sort depth, it sorts from high to low; select the depth sort a second time to sort from low to high.

The Display Mode changes what you can see of the data:

Expanded shows the genotypes at the usual row height, with the sample names in the first column.

Squished shows the genotypes with the rows compressed to maximize the data visible on the page.

You can also adjust the height of the squished row by right-clicking and selecting Change Squished Row Height. You can change the height of the rows in the window provided.

Viewing a VCF File Without Genotypes

If you open a VCF file that does not contain genotypes data, the view will be different, displaying only the bars marking the calls, as shown below.

If the file does contain the sample genotypes, you can hide the genotype information and display only the sites (as in the view below) by unchecking Show Genotypes in the right-click popup menu.