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.

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

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.

Smashing! Thanks for picking up on this old thread.