##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.
Hi! I was successful in creating and uploading several VCF files to the UCSC browser, but trying to view them in "pack" mode gives an error like: vcfTrack.c: gtHapIx 10 out of range [0,9).
Has anyone seen this? It appears to be caused by a failed attempt to draw the dendrogram-- is there anyway to configure the track so that this error is either ignored (i.e., no haplotype determination is attempted) or fixed (i.e., a correct haplotype is determined)? I know it should work because the first time I loaded a VCF track it did-- but now I can't figure out what changed to cause the error.
Thanks!