VCF Files

VCF stands for Variant Call Format, and this file format is used by the 1000 Genomes project to encode SNPs and other structural genetic variants.  The format is further described on the 1000 Genomes project Web site.  VCF calls are available at EBI / NCBI.

Viewing a VCF File with Genotypes


Each bar across the top of the plot shows the allele fraction for a single locus.
The genotypes for each locus in each sample. Dark blue = heterozygous, Cyan = homozygous variant, Grey = reference.  Filtered entries are transparent.

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.

The window size at which VCF data is loaded is proportional to the number of samples.  To change this, 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:

Collapsed removes all the genotypes, leaving only the allele frequency bars.


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. 

Similarly, the popup menu will be more limited, with only the Set Feature Visibility Window... and Remove Track options functional.