The default VCF custom track will display colored bases and will not show clustering unless specified as VCF/tabix in the custom track page.
The following section describes configuration settings available to VCF files compressed and indexed in the Tabix format. This requires VCF manipulation, separate index files, and a web accessible directory to reference from the bigDataUrl track line. For more information on setting up and uploading VCF/Tabix data, click the link on VCF custom track creation.
If the VCF file contains genotype columns for at least two samples (four haplotypes), then a -haplotype sorting display can be configured. This can be useful for determining similarity -between the samples and possible inheritance at a particular loci.
+haplotype sorting display can be configured. This can be useful for determining the similarity +between the samples and inferring inheritance at a particular locus. +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 (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 variants used in clustering), are colored purple.
The haplotype tree can be seen to the left of the track.
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