In this example, you will load a hub that has VCF data described in a hub's trackDb.txt file. First, navigate to the Basic Hub Quick Start Guide and review an introduction to hubs.
Visualizing VCF files in hubs involves creating three text files: hub.txt, genomes.txt, and trackDb.txt. The browser is passed a URL to the top-level hub.txt file that points to the related genomes.txt and trackDb.txt files. The trackDb.txt file contains stanzas for each track that outlines the details and type of each track to display, such as these lines for a VCF file located at the bigDataUrl location:
track vcf1
-bigDataUrl http://hgdownload.soe.ucsc.edu/gbdb/hg19/1000Genomes/ALL.chr21.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz
+bigDataUrl http://hgdownload.gi.ucsc.edu/gbdb/hg19/1000Genomes/ALL.chr21.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz
#Note: there is a corresponding fileName.vcf.gz.tbi in the same above directory
shortLabel chr21 VCF example
longLabel This chr21 VCF file is an example from the 1000 Genomes Phase 1 Integrated Variant Calls Track
type vcfTabix
visibility dense
Note: there is now a useOneFile on hub setting that allows the hub
properties to be specified in a single file. More information about this setting can be found on the
Genome Browser User Guide.
Here is a direct link to the trackDb.txt file to see more information about this example hub, and below is a direct link to visualize the hub in the browser, where this example VCF file displays in dense mode alongside the other tracks in this hub. You can find more Track Hub VCF display options on the Track Database (trackDb) Definition