for a list of Structural Variants (including deletions, duplications, inversions, translocations), either in VCF or BEDPE format, we would like to have the gene annotations, and the lists of the following sets of genes :
-- fusions (if both breakpoints are in exons, introns, utrs)
-- truncations (if only one breakpoint is in exon, intron, utr; and the other breakpoint is in intergenic area)
-- the genes in the areas that are deleted, duplicated, inverted
could we get all these annotations with a package in R/BioC (possibly with VariantAnnotation) ?
I wrote some scripts in perl based on Annovar, although it would be helpful to implement this in R as well.
thanks a lot,