breakpointRanges: Extracting the structural variants as a GRanges.

In PapenfussLab/StructuralVariantAnnotation: Variant annotations for structural variants

Description

Extracting the structural variants as a GRanges.

.breakpointRanges() is an internal function for extracting structural variants as GRanges.

Usage

breakpointRanges(x, ...)

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

.breakpointRanges(
  vcf,
  nominalPosition = FALSE,
  placeholderName = "svrecord",
  suffix = "_bp",
  info_columns = NULL,
  unpartneredBreakends = FALSE,
  inferMissingBreakends = FALSE,
  ignoreUnknownSymbolicAlleles = FALSE
)

Arguments

x	A VCF object
...	Parameters of .breakpointRanges(). See below.
vcf	A VCF object.
nominalPosition	Determines whether to call the variant at the nominal VCF position, or to call the confidence interval (incorporating any homology present). Default value is set to FALSE, where the interval is called based on the CIPOS tag. When set to TRUE, the ranges field contains the nominal variant position only.
placeholderName	Variant name prefix to assign to unnamed variants.
suffix	The suffix to append to variant names.
info_columns	VCF INFO columns to include in the GRanges object.
unpartneredBreakends	Determining whether to report unpartnered breakends. Default is set to FALSE.
inferMissingBreakends	Infer missing breakend records from ALT field of records without matching partners
ignoreUnknownSymbolicAlleles	Ignore unknown symbolic alleles. StructuralVariantAnnotation currently handles INS, INV, DEL, DUP as well as the VCF specifications non-compliant RPL, TRA symbolic alleles.

Details

Structural variants are converted to breakend notation. Due to ambiguities in the VCF specifications, structural variants with multiple alt alleles are not supported. The CIPOS tag describes the uncertainty interval around the position of the breakend. See Section 5.4.8 of https://samtools.github.io/hts-specs/VCFv4.3.pdf for details of CIPOS. If HOMLEN or HOMSEQ is defined without CIPOS, it is assumed that the variant position is left aligned. A breakend on the '+' strand indicates a break immediately after the given position, to the left of which is the DNA segment involved in the breakpoint. The '-' strand indicates a break immediately before the given position, rightwards of which is the DNA segment involved in the breakpoint. Unpaired variants are removed at this stage.

Value

A GRanges object of SVs.

Methods (by class)

• VCF: Extracting structural variants as GRanges.

Examples

vcf.file <- system.file("extdata", "vcf4.2.example.sv.vcf",
                         package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
breakpointRanges(vcf)
breakpointRanges(vcf, nominalPosition=TRUE)

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