+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-accessible, the Genome Browser is able to 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. If you do not have access to a web-accessible server and need hosting space for your VCF files, please see the Hosting section of the Track Hub Help documentation.
The UCSC tools support VCF versions 3.3 and greater.
+If you have VCF trio data, you may be interested in formatting your track as a +Phased Trios track instead. Please see the Phased Trio section +below for more information. +
The typical workflow for generating a VCF custom track is this:
bgzip program:
bgzip my.vcfbgzip command, run it with no arguments to
display the usage message.tabix -p vcf my.vcf.gzbigDataIndex keyword.
This keyword is relevant for Custom Tracks and Track Hubs. You can read more about
bigDataIndex in
the TrackDb Database Definition page.track type=vcfTabix name="My VCF" bigDataUrl=http://myorg.edu/mylab/my.vcf.gzAll options are placed in a single line separated by spaces (lines are broken only for readability here):
track type=vcfTabix bigDataUrl=http://...
hapClusterEnabled=true|false
hapClusterColorBy=altOnly|refAlt|base
hapClusterTreeAngle=triangle|rectangle
hapClusterHeight=N
applyMinQual=true|false minQual=Q
minFreq=F
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. Some are specific to VCF:
hapClusterEnabled true|false # if file has phased genotypes, sort by local similarity
hapClusterColorBy altOnly|refAlt|base # coloring scheme, default altOnly, conditional on hapClusterEnabled
hapClusterTreeAngle triangle|rectangle # draw leaves as < or [, default <, conditional on hapClusterEnabled
hapClusterHeight N # height of track in pixels, default 128, conditional on hapClusterEnabled
applyMinQual true|false # if true, don't display items with QUAL < minQual; default false
minQual Q # minimum value of Q column to display item, conditional on applyMinQual
minFreq F # minimum minor allele frequency to display item; default 0.0 Other optional settings are not specific to VCF, but relevant:
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 vcfPhasedTrio track type is available for users whose VCF contains genotype data from one +to three individuals. The underlying VCF follows the standard VCF format as described above, with +the added caveat that there must be GENOTYPE columns for each of the individuals present. An +example of the trio display is show below for the 1000 Genomes Trio track on Human/GRCh38: +
+
++Unlike a regular genome browser track, Trio tracks display the genome variants of each individual +as two haplotypes; SNPs, small insertions and deletions are mapped to each haplotype based on the +phasing information of the VCF file. Each haplotype is displayed as two separate black lanes for +the browser window region. Each variant is drawn as a vertical dash. Homozygous variants will +show two identical dashes on both haplotype lanes. Phased heterozygous variants are placed on one +of the haplotype lanes and unphased heterozygous variants are displayed in the area between the +two haplotype lanes. +
+ ++After generating this VCF and moving the file to a web accessible location as described above, +then you can use the following required vcfPhasedTrio trackDb settings to get the trio display: +
type vcfPhasedTrio # The track type is required and must be "vcfPhasedTrio"
+bigDataUrl http://url.to.vcfFile The bigDataUrl is rquired
+vcfChildSample GT ID|alias # the Genotype column ID of the "child" sample, with an optional "|" followed by a human readable alias for the ID
+There are also two optional settings for vcfPhasedTrio tracks:
+vcfParentSamples GT ID1|alias1,GT ID2|alias2 # comma separated (no spaces) list of the "parent" samples, with optional aliases
+vcfUseAltSampleNames GT ID # Use the aliases in the display by default instead of the Genotype column ID
+Other optional settings are not specific to VCF, but relevant:
+maxWindowToDraw N # don't display track when viewing more than N bases
+chromosomes chr1,chr2,... # track contains data only on listed reference assembly sequences 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:
browser position chr21:33,034,804-33,037,719
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 The "browser" line above is used to view a small region of chromosome 21 with variants from the .vcf.gz file.
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 click the "submit" button. On the following page, click the "chr21" link in the custom track listing to view the VCF track in the Genome Browser.
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 substitute 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. 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 snp132CommonIn 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
#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 Document page.
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt If you would like to share your VCF data track with a colleague, learn how to create a URL by looking at Example 6 on the custom tracks page.