Configuring VCF tracks

Genome Browser VCF tracks may be configured in a variety of ways to highlight different aspects of the displayed information. Click here for more information on VCF custom track creation.

Configuring the haplotype sorting display

If the VCF file contains genotype columns for at least two samples (four haplotypes), then a haplotype sorting display can be configured.

Enable Haplotype sorting display: When this option is checked, each sample's phased and/or homozygous genotypes are split into haplotypes, clustered by similarity around a central variant, and sorted for display by their position in the clustering tree. The tree (or as much of the tree as space allows) is drawn in the label area next to the track image. Leaf clusters, in which all haplotypes are identical (at least for the span of variants used in clustering), are colored purple. Each variant is drawn as a vertical column, using color to distinguish between reference alleles and alternate alleles of the horizontally running haplotypes. If unchecked, then the display is the same as for VCF without genotypes: a stacked bar graph of the top two alleles, showing the proportion of alleles if allele counts are available. This is checked (enabled) by default.

The following options are applicable only when the haplotype sorting display is enabled:

Haplotype sorting order: Haplotypes are sorted using a distance function that uses a central variant; differences between haplotypes are penalized with weights that decrease for each successive variant away from the central variant. By default, the median variant in the window is used. By clicking on a variant in the display, you will get the option to always use that variant when it is in the current view.

Haplotype coloring scheme: There are three ways that reference and alternate alleles can be colored:

In all coloring modes, if some alleles in a haplotype are undefined, a pale yellowish color is used for those alleles.

Haplotype clustering leaf shape: Leaf clusters are collections of identical haplotypes. By default, they are drawn as open triangles <. They can also be displayed as open rectangles [.

Haplotype sorting display height:Height in pixels of the haplotype sorting display. If this is fewer than the number of haplotypes (2 * the number of genotype columns), some horizontal pixel rows must represent multiple haplotypes; differing haplotypes' colors will be combined according to the selected coloring scheme.

Filtering out variants

Variants can be filtered out of the display according to several properties:

When you have finished making your configuration changes, click the Submit button to return to the annotation track display page.