How Best To Add Custom Variation Track To Ucsc Browser?

Question

[Ian]

I have generated sequence variants (SNPs/INDELs) by NGS resequencing and would like to display them on the UCSC browser (I have resequenced against a UCSC reference genome). Obviously i could use BED files for SNPs, but does anyone know the best way to upload SNPs/INDELS in a custom track?

Answer 1

[Alastair Kerr]

I use an in-house galaxy server for all my coordinate data. It provides links to display your data uploaded into your history on both UCSC and ensembl automatically - assuming you have filled in the metadata for the species build for the correct species.

[Ian]

It isn't that i don't know how to display my own data in UCSC, but what is the best way to present SNP, insertion and deletions relative to the reference sequence. SNPs are simple as they are just simple coordinates, but INDELS are a bit more of a challenge. Thanks anyway.

[Alastair Kerr]

Why not use an use an interval or wiggle file: chromosome, start, stop and value, where value = the size of the indel, negative for deletion, positive for insertion

[Ian]

Interesting! The samtools pileup format does anchor insertions and deletions to coordinates of the reference genome. If there isn't an existing method, then i will certainly pursue this.

Answer 2

[brentp]

I wrote up one method of doing this here:

##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.

view raw gistfile1.md hosted with ❤ by GitHub

UCSC recently added the ability to render VCF as a custom track.

[Ian]

Smashing! Thanks for picking up on this old thread.

Answer 3

[Ian]

The helpful people from UCSC browser sent me a link, the bottom of which describes the 'Personal Genome SNP format' which can be used as a custom track. But this does not appear to handle INDELS. This is currently only for the TEST browser.