findInsDupOverlaps: Finds duplication events that are reported as inserts. As...

In StructuralVariantAnnotation: Variant annotations for structural variants

Description

WARNING: this method does not yet 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

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