extractBreakpointSequence {StructuralVariantAnnotation} | R Documentation |
Extracts the breakpoint sequence.
extractBreakpointSequence(gr, ref, anchoredBases, remoteBases = anchoredBases)
gr |
breakpoint GRanges |
ref |
Reference BSgenome |
anchoredBases |
Number of bases leading into breakpoint to extract |
remoteBases |
Number of bases from other side of breakpoint to extract |
The sequence is the sequenced traversed from the reference anchor bases to the breakpoint. For backward (-) breakpoints, this corresponds to the reverse compliment of the reference sequence bases.
Breakpoint sequence around the variant position.