157d7eb9f2765db7651e12c14233c56fa7205e96 mspeir Thu Sep 17 14:46:12 2026 -0700 VCF help: add the two settings the sweep missed, and fix a value order, refs #38010 The earlier commit left out sampleMetadataFile and showHardyWeinberg on the grounds that nothing in the tree reads them. Both are read: hgc/vcfClick.c loads the metadata file in vcfGenotypeTable, and reads showHardyWeinberg with cartOrTdbBoolean in vcfGenotypesDetails. Neither call is gated on track type, so both also apply to vcfPhasedTrio, which tagTypes.tab had not allowed; that is corrected here too. sampleColorFile and showHardyWeinberg had no entry in trackDbLibrary.shtml, so they were missing from the trackDb doc pages as well. Both get a blurb, a row in trackDbDoc.html and trackDbHub.v3.html, and a changes.html note. sampleColorFile is the last VCF setting that was recognized but undocumented. vcf.html and the three trackDb doc files listed vcfPhasedColorBy as mendelDiff|deNovo|function|noColor. vcfUi.c prints the radio buttons in the opposite order, so the lists now read noColor|function|deNovo|mendelDiff, the way hapClusterColorBy already matches its own buttons. trackDbSettings.yaml and .json are regenerated. They also pick up minAc, vcfDoMinAc and vcfPhasedColorBy, which were documented earlier in this series without a regen. Found in the v504 code review, #38354. 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 d64733d79ff..a0a4da64f5a 100755 --- src/hg/htdocs/goldenPath/help/vcf.html +++ src/hg/htdocs/goldenPath/help/vcf.html @@ -174,30 +174,32 @@ <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|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>sampleMetadataFile </strong><em>url </em> # extra sample columns, added to the genotype table on the details page +<strong>showHardyWeinberg </strong><em>true|false </em> # show Hardy-Weinberg equilibrium on the details page; default false <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> @@ -239,31 +241,31 @@ 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 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 +<strong>vcfPhasedColorBy </strong><em>noColor|function|deNovo|mendelDiff</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