extractBreakpointSequence: Extracts the breakpoint sequence.

In StructuralVariantAnnotation: Variant annotations for structural variants

Description

Extracts the breakpoint sequence.

Usage

extractBreakpointSequence(gr, ref, anchoredBases, remoteBases = anchoredBases)

Arguments

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

Details

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.

Value

Breakpoint sequence around the variant position.

StructuralVariantAnnotation documentation built on Nov. 8, 2020, 5:43 p.m.