VCF+tabix Track Format
3. | Variant Call Format (VCF) is a flexible and extendable line-oriented text format developed by the 1000 Genomes Project for releases of single nucleotide variants, indels, copy number variants and structural variants discovered by the project. When a VCF file is compressed and indexed using tabix, and made web-accesible, the Genome Browser can fetch only the portions of the file necessary to display items in the viewed region. This makes it possible to display variants from files that are so large that the connection to UCSC would time out when attempting to upload the whole file to UCSC. Both the VCF file and its tabix index file remain on your web-accessible server (http, https, or ftp), not on the UCSC server. UCSC temporarily caches the accessed portions of the files to speed up interactive display. Please note that UCSC only supports VCF versions 3.3, 3.4, 4.0 and 4.1. The typical workflow for generating a VCF custom track is this: If you haven't done so already, download and build the tabix and bgzip programs. Test your installation by running `tabix` with no command line arguments; it should print a brief usage message. For help with `tabix`, please contact the samtools-help mailing list (tabix is part of the samtools project). Create VCF or convert another format to VCF. Items must be sorted by genomic position. Compress your .vcf file using the `bgzip` program:
       bgzip my.vcf
4. For more information about the bgzip command, run `bgzip` with no other arguments. Create a tabix index file for the bgzip-compressed VCF (.vcf.gz):
       tabix -p vcf my.vcf.gz
6. The tabix command appends `.tbi` to `my.vcf.gz`, creating a binary index file `my.vcf.gz.tbi` with which genomic coordinates can quickly be translated into file offsets in `my.vcf.gz`. Move both the compressed VCF file and tabix index file (`my.vcf.gz` and `my.vcf.gz.tbi`) to an http, https, or ftp location. Construct a custom track using a single track line. The most basic version of the track line will look something like this:
       track type=vcfTabix name="My VCF" bigDataUrl=http://myorg.edu/mylab/my.vcf.gz
Again, in addition to http://myorg.edu/mylab/my.vcf.gz, the associated index file http://myorg.edu/mylab/my.vcf.gz.tbi must also be available at the same location. Paste the custom track line into the text box in the custom track management page, click submit and view in the Genome Browser. ### Parameters for VCF custom track definition lines All options are placed in a single line separated by spaces (lines are broken only for readability here):
      track type=vcfTabix bigDataUrl=http://...
         name=track_label description=center_label
         visibility=display_mode priority=priority
         db=db maxWindowToDraw=N
         chromosomes=chr1,chr2,...
Note if you copy/paste the above example, you must remove the line breaks. Click here for a text version that you can paste without editing. The track type and bigDataUrl are REQUIRED:
      type=vcfTabix bigDataUrl=http://myorg.edu/mylab/my.vcf.gz
The remaining settings are OPTIONAL.
      name            track label                 # default is "User Track"
      description     center label                # default is "User Supplied Track"
      visibility      squish|pack|full|dense|hide # default is hide (will also take numeric values 4|3|2|1|0)
      priority        N                           # default is 100
      db              genome database             # e.g. hg19 for Human Feb. 2009 (GRCh37)
      maxWindowToDraw N                           # don't display track when viewing more than N bases
      chromosomes     chr1,chr2,...               # track contains data only on listed reference assembly sequences
The VCF track configuration help page describes the VCF track configuration page options. ### Example One In this example, you will create a custom track for an indexed VCF file that is already on a public server — variant calls generated by the 1000 Genomes Project. The line breaks inserted here for readability must be removed before submitting the track line:
    track type=vcfTabix name="VCF Example One" description="VCF Ex. 1: 1000 Genomes phase 1 interim SNVs"
        chromosomes=chr21 maxWindowToDraw=200000
        db=hg19 visibility=pack
        bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz
Include the following "browser" line to view a small region of chromosome 21 with variants from the .vcf.gz file: `browser position chr21:33,034,804-33,037,719` Note if you copy/paste the above example, you must remove the line breaks (or, click here for a text version that you can paste without editing). Paste the "browser" line and "track" line into the custom track management page for the human assembly hg19 (Feb. 2009), then press the submit button. On the following page, press the chr21 link in the custom track listing to view the VCF track in the Genome Browser. ### Example Two In this example, you will create compressed, indexed VCF from an existing VCF text file. First, save this VCF file vcfExampleTwo.vcf to your machine. Perform steps 1 and 3-7 in the workflow described above, but substituting `vcfExampleTwo.vcf` for `my.vcf`. On the custom track management page, click the "add custom tracks" button if necessary and make sure that the genome is set to Human and the assembly is set to Feb. 2009 (hg19) before pasting the track line and submitting. This track line is a little nicer than the one shown in step 6, but remember to remove the line breaks that have been added to the track line for readability (or, click here for a text version that you can paste without editing):
    track type=vcfTabix name="VCF Example Two" bigDataUrl=http://myorg.edu/mylab/vcfExampleTwo.vcf.gz
        description="VCF Ex. 2: More variants from 1000 Genomes" visibility=pack
        db=hg19 chromosomes=chr21

    browser position chr21:33,034,804-33,037,719
    browser pack snp132Common
### Sharing Your Data with Others If you would like to share your VCF data track with a colleague, learn how to create a URL by looking at Example 11 on this page. |