6d02024d6f5b80437784b274ff2ccf6940dde976 mspeir Wed Sep 9 15:08:26 2026 -0700 VCF help: document geneTrack, the function coloring scheme, and vcfPhasedColorBy, refs #38010 The rest of the settings vcfUi.c reads from trackDb but neither help page mentioned. geneTrack (vcfUi.c:269 and :681) is the gate for the functional-effect coloring in both the haplotype display and the trio display: the radio button is only printed when the setting is non-empty. Nothing on either page said so, so the scheme was undiscoverable and its absence looked like a bug. hapClusterColorBy therefore has four values, not the three both pages listed -- hgVcfTrackHelp.html went as far as saying "There are three ways that reference and alternate alleles can be colored" above three bullets. Add the fourth, in the order vcfCfgHapClusterColor prints the buttons, and add function to the value lists in vcf.html. vcfPhasedColorBy (mendelDiff|deNovo|function|noColor) was documented nowhere at all, not even in trackDbLibrary.shtml, though vcf.html already described what it does in the alt text of the trio screenshot. Add it to the trio settings. Both settings tables needed a wider value column to fit, so those rows are repadded; no wording in them changed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/goldenPath/help/vcf.html src/hg/htdocs/goldenPath/help/vcf.html index cac60b53e20..d64733d79ff 100755 --- src/hg/htdocs/goldenPath/help/vcf.html +++ src/hg/htdocs/goldenPath/help/vcf.html @@ -1,341 +1,343 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser VCF+tabix Track Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>VCF+tabix Track Format</h1> <p> <a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41" target="_blank">Variant Call Format</a> (VCF) is a flexible and extendable line-oriented text format developed by the <a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project</a> (now maintained by the <a href="http://ga4gh.org/#/fileformats-team" target="_blank">GA4GH</a>) 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 <a href="http://samtools.sourceforge.net/tabix.shtml" target="_blank">tabix</a>, 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 <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation.</p> <p>The UCSC tools support VCF versions 3.3 and greater.</p> <p>If you have VCF trio data, you may be interested in formatting your track as a <a href="#trio">Phased Trios</a> track as described below. <h2>VCF Format </h2> <p> VCF is an all-purpose format for defining variants of all types: SNVs, CNVs and translocations relative to a reference assembly. It can annotate all the variants in an individual as well as a population. Typically, a VCF file is too large to load directly into a custom track on the Browser and must be loaded as binary tabix-indexed file as described below. The full specification of VCF is found in <a href = "http://samtools.github.io/hts-specs/VCFv4.3.pdf" target = _blank>documents on github</a>. <p>Here is a look at an example from that file showing a few rows of data for three samples. Details and descriptions of the data fields are in the <a href = "http://samtools.github.io/hts-specs/VCFv4.3.pdf" target = _blank>.pdf</a>. The data here can be pasted directly into hg18 human assembly on the Genome Browser. We have added two lines at the top of the entry that are not in the official example to make the display work in the Browser. </p> <p> Note that the first data field, identifying the chromosome, is in official VCF format which does not include the "chr" usually associated with Genome Browser chrom names. Either version will work in the Browser. </p> <p> <pre> track type=vcf name="vcf example" description="three samples in a vcf" db=hg18 visibility="full" browser position chr20:1-1306000 ##fileformat=VCFv4.2 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta ##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x> ##phasing=partial ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> ##FILTER=<ID=q10,Description="Quality below 10"> ##FILTER=<ID=s50,Description="Less than 50% of samples have data"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 </pre> </p> <a name="generating"></a> <h2>Generating a VCF track</h2> <p> The typical workflow for generating a VCF custom track is this:</p> <ol> <li> If you haven't done so already, <a href="http://sourceforge.net/projects/samtools/files/tabix/" target="_blank"> download</a> and build the <a href="http://samtools.sourceforge.net/tabix.shtml" target="_blank">tabix and bgzip</a> 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 <a href="https://lists.sourceforge.net/lists/listinfo/samtools-help" target="_blank">samtools-help mailing list</a> (tabix is part of the samtools project).</li> <li> Create VCF or convert another format to VCF. Items must be sorted by genomic position.</li> <li> Compress your <em>.vcf</em> file using the <code>bgzip</code> program: <pre><code>bgzip my.vcf</code></pre> For more information about the <code>bgzip</code> command, run it with no arguments to display the usage message.</li> <li> Create a tabix index file (<code>.tbi</code> or <code>.csi</code>) for the bgzip-compressed VCF (<em>.vcf.gz</em>). By default, the tabix command appends <em>.tbi</em> to the <em>my.vcf.gz</em> filename, creating a binary index file named <em>my.vcf.gz.tbi</em> with which genomic coordinates can quickly be translated into file offsets in <em>my.vcf.gz</em>: <pre><code>tabix -p vcf my.vcf.gz</code></pre> The tabix (<code>.tbi</code>) and BAI index formats can handle individual chromosomes up to 512 Mbp (2^29 bases) in length. If your input file contains data lines with start or end positions greater than 512 Mbp, you will need to use a CSI (<code>.csi</code>) index instead. <pre><code>tabix --csi -p vcf my.vcf.gz</code></pre> </li> <li> Move both the compressed VCF file (<em>my.vcf.gz</em>) and index file (<em>my.vcf.gz.tbi</em> or <em>my.vcf.gz.csi</em>) to an http, https, or ftp location. Note that the Genome Browser looks for an index file with the same URL as the VCF file with the .tbi or .csi suffix added. <br><br> If your hosting site does not use the filename as the URL link, you will have to specifically call the location of this .vcf.tbi/csi index file with the <code>bigDataIndex</code> keyword. You can read more about <em>bigDataIndex</em> in <a href="trackDb/trackDbHub.html#bigDataIndex">the TrackDb Database Definition page</a>.</li> <li> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. The basic version of the track line will look something like this: <pre><code>track type=vcfTabix name="My VCF" bigDataUrl=<em>http://myorg.edu/mylab/my.vcf.gz</em></code></pre> Again, in addition to <em>http://myorg.edu/mylab/my.vcf.gz</em>, the associated index file <em>http://myorg.edu/mylab/my.vcf.gz.tbi</em> must also be available at the same location. If the file is in a different location or uses a different filename, then use the <em>bigDataIndex</em> attribute in the track line to point to the index file. <pre><code>track type=vcfTabix name="My VCF" bigDataUrl=<em>http://myorg.edu/mylab/my.vcf.gz</em> bigDataIndex=<em>http://myorg.edu/someOtherDirectory/myvcf.gz.tbi</em></code></pre> </li> <li> Paste the custom track line into the text box in the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a>, click "submit" and view in the Genome Browser.</li> </ol> <h2>Parameters for VCF custom track definition lines</h2> <p> All options are placed in a single line separated by spaces (lines are broken only for readability here):</p> <pre><code><strong>track type=vcfTabix bigDataUrl=</strong><em>http://...</em> <strong>hapClusterEnabled=</strong><em>true|false</em> - <strong>hapClusterColorBy=</strong><em>altOnly|refAlt|base</em> + <strong>hapClusterColorBy=</strong><em>altOnly|function|refAlt|base</em> <strong>hapClusterTreeAngle=</strong><em>triangle|rectangle</em> <strong>hapClusterHeight=</strong><em>N</em> <strong>applyMinQual=</strong><em>true|false</em> <strong>minQual=</strong><em>Q</em> <strong>minFreq=</strong><em>F</em> <strong>name=</strong><em>track_label</em> <strong>description=</strong><em>center_label</em> <strong>visibility=</strong><em>display_mode</em> <strong>priority=</strong><em>priority</em> <strong>db=</strong><em>db</em> <strong>maxWindowToDraw=</strong><em>N</em> <strong>chromosomes=</strong><em>chr1,chr2,...</em> </code></pre> <p> Note if you copy/paste the above example, you must remove the line breaks. Click <a href="examples/vcfExample.txt">here</a> for a text version that you can paste without editing.</p> <p> The track type and bigDataUrl are REQUIRED:</p> <pre><code><strong>type=vcfTabix bigDataUrl=</strong><em>http://myorg.edu/mylab/my.vcf.gz</em></strong> </code></pre> <p> The remaining settings are OPTIONAL. Some are specific to VCF:</p> <pre><code><strong>hapClusterEnabled </strong><em>true|false </em> # if file has phased genotypes, sort by local similarity -<strong>hapClusterColorBy </strong><em>altOnly|refAlt|base </em> # coloring scheme, default altOnly, conditional on hapClusterEnabled +<strong>hapClusterColorBy </strong><em>altOnly|function|refAlt|base</em> # coloring scheme, default altOnly, conditional on hapClusterEnabled <strong>hapClusterTreeAngle </strong><em>triangle|rectangle </em> # draw leaves as < or [, default <, conditional on hapClusterEnabled <strong>hapClusterHeight </strong><em>N </em> # height of track in pixels, default 128, conditional on hapClusterEnabled +<strong>geneTrack </strong><em>track name </em> # gene track used by the function coloring scheme; without it that scheme is not offered <strong>applyMinQual </strong><em>true|false </em> # if true, don't display items with QUAL < minQual; default false <strong>minQual </strong><em>Q </em> # minimum value of Q column to display item, conditional on applyMinQual <strong>minFreq </strong><em>F </em> # minimum minor allele frequency to display item; default 0.0 </code></pre> <p> These VCF settings are also recognized. They are used mainly in track hubs and are rarely needed in a custom track line:</p> <pre><code><strong>hapClusterMethod </strong><em>centerWeighted|fileOrder|treeFile url</em> # haplotype sort order, default centerWeighted <strong>sampleColorFile </strong><em>url </em> # sample-to-color table, used with hapClusterMethod treeFile <strong>minAc </strong><em>N </em> # minimum alternate allele count to display item; default 0 <strong>vcfDoQual </strong><em>true|false </em> # show the QUAL controls on the configuration page; default true <strong>vcfDoFilter </strong><em>true|false </em> # show the FILTER controls; default true <strong>vcfDoMaf </strong><em>true|false </em> # show the allele frequency control; default true <strong>vcfDoMinAc </strong><em>true|false </em> # show the allele count control; default true</code></pre> <p> Other optional settings are not specific to VCF, but relevant:</p> <pre><code><strong>name </strong><em>track label </em> # default is "User Track" <strong>description </strong><em>center label </em> # default is "User Supplied Track" <strong>visibility </strong><em>squish|pack|full|dense|hide</em> # default is hide (will also take numeric values 4|3|2|1|0) <strong>priority </strong><em>N </em> # default is 100 <strong>db </strong><em>genome database </em> # e.g. hg19 for Human Feb. 2009 (GRCh37) <strong>maxWindowToDraw </strong><em>N </em> # don't display track when viewing more than N bases <strong>chromosomes </strong><em>chr1,chr2,... </em> # track contains data only on listed reference assembly sequences </code></pre> <p> The <strong>visibility</strong> setting controls what the track draws, not just how tightly it is packed. In <strong>pack</strong> or <strong>squish</strong> mode, a VCF that has genotype columns for two or more samples is drawn as the haplotype sorting display, in which each sample's haplotypes run horizontally across the image. In <strong>full</strong> mode the track draws one row per variant, and in <strong>dense</strong> mode it collapses every variant onto a single row. The hapCluster settings above are ignored in those two modes, and also whenever <strong>hapClusterEnabled</strong> is false or the file has no genotypes.</p> <p> The <a target="_blank" href="hgVcfTrackHelp.html">VCF track configuration</a> help page describes the VCF track configuration page options.</p> <a name="trio"></a> <h2>Phased Trio format</h2> <p>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 shown below for the <a href="../../cgi-bin/hgTrackUi?db=hg38&g=tgpTrios">1000 Genomes Trio track on Human/GRCh38</a>: </p> <div class="text-center"> <a href="../../cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=dschmelt&hgS_otherUserSessionName=tgpTrios"> <img width="80%" height="80%" src="../../images/trioExample.png" alt="3 VCF Phased Trio tracks along with the GENCODE v32 genes from the Human/GRCh38 assembly. Each of two diploid haplotypes for each individual in a trio is drawn as a black lane, with snps as vertical ticks on the haplotype they fall on. Ticks are shaded blue,red,green or black according to their predicted functional effect."></a> </div> <p> 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 on two separate, horizontal black lines across the browser window. Each variant is drawn as a vertical dash. Homozygous variants will show two identical dashes on both haplotype lines. Phased heterozygous variants are placed on one of the haplotype lanes and unphased heterozygous variants are displayed in the area between the two haplotype lines. </p> <p> Follow the steps for a normal VCF file, including moving the file to a web accessible location and generating a tabix index file, then use the following required vcfPhasedTrio trackDb settings to view the trio display: <pre><code><strong>type </strong><em>vcfPhasedTrio </em> # The track type is required and must be "vcfPhasedTrio" <strong>bigDataUrl </strong><em>http://url.to.vcfFile </em> # The bigDataUrl is required <strong>vcfChildSample </strong><em>GT ID|alias </em> # the Genotype column ID of the "child" sample, with an optional "|" followed by a human readable alias for the ID </code></pre> -<p>There are also two optional settings for vcfPhasedTrio tracks:</p> +<p>There are also three optional settings for vcfPhasedTrio tracks:</p> <pre><code><strong>vcfParentSamples </strong><em>GT ID1|alias1,GT ID2|alias2 </em> # comma separated (no spaces) list of the "parent" samples, with optional aliases <strong>vcfUseAltSampleNames </strong><em>GT ID </em> # Use the aliases in the display by default instead of the Genotype column ID +<strong>vcfPhasedColorBy </strong><em>mendelDiff|deNovo|function|noColor</em> # allele coloring scheme, default noColor; function also requires geneTrack </code></pre> <p>Other optional settings are not specific to VCF, but relevant:</p> <pre><code><strong>maxWindowToDraw </strong><em>N </em> # don't display track when viewing more than N bases <strong>chromosomes </strong><em>chr1,chr2,... </em> # track contains data only on listed reference assembly sequences </code></pre> <h2>Examples</h2> <h3>Example #1</h3> <p> 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 <a href="http://1000genomes.org/" target="_blank">1000 Genomes Project</a>. The line breaks inserted here for readability must be removed before submitting the track line:</p> <pre><code>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 </code></pre> <p> The "browser" line above is used to view a small region of chromosome 21 with variants from the <em>.vcf.gz</em> file.</p> <p> Note if you copy/paste the above example, you must remove the line breaks (or, click <a href="examples/vcfExampleOne.txt">here</a> for a text version that you can paste without editing).</p> <p> Paste the "browser" line and "track" line into the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a> 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.</p> <h3>Example #2</h3> <p> In this example, you will create compressed, indexed VCF from an existing VCF text file. First, save this VCF file -- <em><a href="examples/vcfExampleTwo.vcf" target="_blank">vcfExampleTwo.vcf</a></em> -- to your machine. Perform steps 1 and 3-7 in the workflow described above, but substitute <em>vcfExampleTwo.vcf</em> for <em>my.vcf</em>. On the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a>, 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 <a href="examples/vcfExampleTwo.txt">here</a> for a text version that you can paste without editing):</p> <pre><code>track type=vcfTabix name="VCF Example Two" bigDataUrl=<em>http://myorg.edu/mylab/vcfExampleTwo.vcf.gz</em> 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</code></pre> <h3>Example #3</h3> <p> In this example, you will load a hub that has VCF data described in a hub's trackDb.txt file. First, navigate to the <a href="hubQuickStart.html" target="_blank">Basic Hub Quick Start Guide</a> and review an introduction to hubs.</p> <p> Visualizing VCF files in hubs involves creating three text files: <em>hub.txt</em>, <em>genomes.txt</em>, and <em>trackDb.txt</em>. The browser is passed a URL to the top-level <em>hub.txt</em> file that points to the related <em>genomes.txt</em> and <em>trackDb.txt</em> files. The <em>trackDb.txt</em> 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:</p> <pre><code>track vcf1 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 </code></pre> <p> <b>Note:</b> there is now a <code>useOneFile on</code> hub setting that allows the hub properties to be specified in a single file. More information about this setting can be found on the <a href="./hgTracksHelp.html#UseOneFile" target="_blank">Genome Browser User Guide</a>.</p> <p> Here is a direct link to the <em><a href="examples/hubDirectory/hg19/trackDb.txt" target="_blank">trackDb.txt</a></em> 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 <a href="trackDb/trackDbHub.html#vcfTabix" target="_blank">Track Database (trackDb) Definition Document</a> page.</p> <pre><code><a href="../../cgi-bin/hgTracks?db=hg19&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt</a> </code></pre> <h2>Sharing Your Data with Others</h2> <p> If you would like to share your VCF data track with a colleague, learn how to create a URL by looking at <strong>Example 6</strong> on the <a href="customTrack.html#SHARE">custom tracks</a> page.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->