findInsDupOverlaps {StructuralVariantAnnotation}R Documentation

Finds duplication events that are reported as inserts. As sequence alignment algorithms do no allow backtracking, long read-based variant callers will frequently report small duplication as insertion events. Whilst both the duplication and insertion representations result in the same sequence, this representational difference is problematic when comparing variant call sets.

Description

WARNING: this method does not check that the inserted sequence actually matched the duplicated sequence.

Usage

findInsDupOverlaps(query, subject, maxgap = -1L, maxsizedifference = 0L)

Arguments

query

a breakpoint GRanges object

subject

a breakpoint GRanges object

maxgap

maximum distance between the insertion position and the duplication

maxsizedifference

maximum size difference between the duplication and insertion.

Value

Hits object containing the ordinals of the matching breakends in the query and subject


[Package StructuralVariantAnnotation version 1.10.1 Index]