##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.
Thanks for implementing!
I've tried VCFs from samtools and freebayes and they both render fine.
Not sure what exactly you mean by the haplotype clustering, but (in my opinion) support for some type of visualization of genotypes would be great!
I generally have multiple samples in my VCF's.