I'm currently working on a structural variants calling pipeline on NGS data from cancer patients, specifically the annotation and intersection/joining with different databases.
While the vast majority of the structural variants I find, including indels of all sizes, CNVs, ITDs, duplications & inversions, are successfully joined+intersected and annotated, translocations are yet to be either annotated or successfully found in the databases even if i'm extending the search ranges in their supposed chromosomes.
Has anyone experienced the same difficulty?
I'm using VEP for annotation and the databases are Cosmic, DGV & DbVar.
I will greatly appreciate your suggestions on annotators and databases suitable for translocations, preferably related to cancer but not necessarily.
Thank you, Alon