I want to know if there is some kind of pipeline i can use in order to annotate a given list of structural variants detected by NGS.
specifically, i just ran Breakdancer on a paired end sequencing data and recieved the output specifying the different types of predicted variations (insertions / deletions / inversions / translocations) example :
1 1413910 9+0- 1 1452528 0+10- DEL 38636 99
1 1588571 0+17- 1 1653965 17+0- ITX 64960 99
the columns are : chr1, position1, supportingreads(forward/reverse), chr2, position2, supportingreads(forward/reverse), variationtype, variationsize, quality
i basically want to annotate these variants in regards to gene name, exon/intron, transcription binding sites, ncRNA (miRNA) and any other known feature regarding the genetic region affected by them.
is there a known tool for this? if not, i would appreciate any suggestions on how to perform such a task (for example some sort of outline for a workflow i can build)