breakendRanges: Extracting unpartnered breakend structural variants as a...

In PapenfussLab/StructuralVariantAnnotation: Variant annotations for structural variants

Description

Extracting unpartnered breakend structural variants as a GRanges

Usage

breakendRanges(x, ...)

## S4 method for signature 'VCF'
breakendRanges(x, ...)

Arguments

x	A VCF object.
...	Parameters of .breakpointRanges(). See breakpointRanges for more details.

Details

The VCF standard supports single breakends where a breakend is not part of a novel adjacency and lacks a mate. This function supports parsing single breakends to GRanges, where a dot symbol is used in the ALT field to annotate the directional information. Single breakends provide insights to situations when one side of the structural variant is not observed, due to e.g. low mappability, non-reference contigs, complex multi-break operations, etc. See Section 5.4.9 of https://samtools.github.io/hts-specs/VCFv4.3.pdf for details of single breakends.

Value

A GRanges object of SVs.

Methods (by class)

• VCF: Extracting unpartnered structural variants as GRanges.

Examples

vcf.file <- system.file("extdata", "gridss.vcf",
                         package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
breakendRanges(vcf)
breakendRanges(vcf, nominalPosition=TRUE)

PapenfussLab/StructuralVariantAnnotation documentation built on Dec. 25, 2021, 1:20 a.m.