Hi GENIE team! Is it possible to have breakpoints for the structural variants? Post-processed data include only (I think) gene partners but not breakpoint details (these are NA in cBioPortal).
It would be very helpful to have the breakpoints coordinates (or at least which introns/exons are involved in each gene).
Thank you so much!!!
Biagio Ricciuti DFCI
Created by Biagio Ricciuti biagio.ricciuti Dear @biagio.ricciuti,
As an update, the structural variant file format (data_sv.txt) used in GENIE does accept breakpoint information, but the previous file format (data_fusions.txt) did not. Since we created the initial structural variant file directly from the fusions file, this first release of the structural variant file did not include breakpoints.
Breakpoint information may be available in future releases.
Best,
Chelsea Dear @biagio.ricciuti,
We will discuss the possibility of adding breakpoints for structural variants. Thank you for using the GENIE dataset!
Best,
Chelsea