##VCF in UCSC
Note, documentation is now available here: http://genome.ucsc.edu/goldenPath/help/vcf.html
It's possible to display a vcf in the UCSC genome browser
First grab tabix from sourceforge:
svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/tabix
cd tabix && make
Then add that directory to your PATH.
bgzip the vcf and index with tabix
bgzip t.vcf
tabix -p vcf t.vcf.gz
Put t.vcf.gz
and t.vcf.gz.tbi
in a web directory. Along with a bed
file, t.bed
with contents:
track type=vcfTabix name="$NAME" visibility=full bigDataUrl="http://example.com/path.to/t.vcf.gz"
Adjusting the paths to match your server.
Note the type is vcfTabix
Finally, point your web-browser to: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr11:1240203-1247497&hgt.customText=http://example.com/path.to/t.bed
and the variant track will be visible.
Of course as soon as I seek help, I figure out the issue. The gtHapIx error was caused by incorrect AC,AN values in the INFO column; I suspected that was the case early on, and I fixed the file with the vcf-tools fix-ac-an function. However, upon reloading the files, the error persisted. It looks like, though, this was a caching issue, not a processing issue-- after I deleted the track and reloaded from scratch, the issue was fixed. My error. If we want to take something away here, though, perhaps you could add to the error message a helpful, "Make sure your VCF key=value pairs like AC and AN are correct." :) Thanks!