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.
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.