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?
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.
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.
I wrote up one method of doing this here: https://gist.github.com/1232981
UCSC recently added the ability to render VCF as a custom track.
The helpful people from UCSC browser sent me a link http://genome-test.cse.ucsc.edu/FAQ/FAQformat.html 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.
