I am developing a tool which would take a gene list as input, and the output would be a VCF including fusion variants involving the genes of interest.
I am going to use Mitelman database which has a comprehensive curation of fusions from published literatures. However, the breakpoints are in cytoband format, i.e., 19p13, rather than a genomic coordinate, such like chr1 10099767.
My questions are: - Are there any other comprehensive databases that you would recommend which have precise breakpoints information in genomic coordinates format? (I tried COSMIC, TCGA, the fusion files are as not comprehensive, seems many well-known fusions are missing from those). - If Mitelman turns out to be the most comprehensive database, how would you suggest I can find corresponding genomic coordinates for the fusions in mitelman in a easy way?