bf0173ba67b220a32d0f58bdce669db1060ec53a dschmelt Thu Oct 1 16:15:44 2020 -0700 CR fix refs #26267 diff --git src/hg/htdocs/goldenPath/help/vcf.html src/hg/htdocs/goldenPath/help/vcf.html index 9c63ce8..e83cb45 100755 --- src/hg/htdocs/goldenPath/help/vcf.html +++ src/hg/htdocs/goldenPath/help/vcf.html @@ -140,31 +140,31 @@ <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 rquired +<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> <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 </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/"