198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/vcf.html src/hg/htdocs/goldenPath/help/vcf.html index 99d53b85774..92d8ff19448 100755 --- src/hg/htdocs/goldenPath/help/vcf.html +++ src/hg/htdocs/goldenPath/help/vcf.html @@ -185,31 +185,31 @@ <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> 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 show below for the +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