24e9efad07acca531ab9640912d32034b6086145 kuhn Wed Jan 6 17:25:52 2021 -0800 added clarification that hg18 is a human assembly diff --git src/hg/htdocs/goldenPath/help/vcf.html src/hg/htdocs/goldenPath/help/vcf.html index c74afe6..cb4135b 100755 --- src/hg/htdocs/goldenPath/help/vcf.html +++ src/hg/htdocs/goldenPath/help/vcf.html @@ -30,31 +30,31 @@ <h2>VCF Format </h2> <p> VCF is an all-purpose format for defining variants of all types: SNVs, CNVs and translocations. 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 on the Genome Browser. We +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