Package: StructuralVariantAnnotation 1.23.0

Daniel Cameron

StructuralVariantAnnotation: Variant annotations for structural variants

StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Authors:Daniel Cameron [aut, cre], Ruining Dong [aut]

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StructuralVariantAnnotation.pdf |StructuralVariantAnnotation.html✨
StructuralVariantAnnotation/json (API)
NEWS

# Install 'StructuralVariantAnnotation' in R:
install.packages('StructuralVariantAnnotation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:StructuralVariantAnnotation-1.23.0(bioc 3.21)StructuralVariantAnnotation-1.22.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dataimportsequencingannotationgeneticsvariantannotation

6.26 score 2 packages 102 scripts 629 downloads 2 mentions 20 exports 82 dependencies

Last updated 4 months agofrom:0faca97341. Checks:8 OK. Indexed: yes.

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Doc / VignettesOKFeb 18 2025
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R-4.5-macOKFeb 18 2025
R-4.5-linuxOKFeb 18 2025
R-4.4-winOKFeb 18 2025
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R-4.3-winOKFeb 18 2025
R-4.3-macOKFeb 18 2025

Exports:breakendRangesbreakpointgr2bedpebreakpointgr2pairsbreakpointRangescalculateReferenceHomologycountBreakpointOverlapsextractBreakpointSequenceextractReferenceSequencefindBreakpointOverlapsfindInsDupOverlapsfindTransitiveCallshasPartnerisStructuralisSymbolicnumtDetectpairs2breakpointgrpartnerrtDetectsimpleEventLengthsimpleEventType

Dependencies:abindAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfansifastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpwalignR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryaml

StructuralVariantAnnotation Quick Overview

Ruining Dong, Daniel Cameron

Rendered fromvignettes.Rmdusingknitr::rmarkdownon Feb 18 2025.

Last update: 2021-08-05
Started: 2019-02-17

Readme and manuals

Help Manual

Help pageTopics
Adjusting the nominal position of a pair of partnered breakpoint.align_breakpoints
Extracting unpartnered breakend structural variants as a GRangesbreakendRanges breakendRanges,VCF-method
Converting breakpoint GRanges to BEDPE-like dataframebreakpointgr2bedpe
Converts a breakpoint GRanges object to a Pairs objectbreakpointgr2pairs pairs2breakpointgr
Converts the given breakpoint GRanges object to VCF format in breakend notation.breakpointGRangesToVCF
Extracting the structural variants as a GRanges..breakpointRanges breakpointRanges breakpointRanges,VCF-method
Calculates the length of inexact homology between the breakpoint sequence and the referencecalculateReferenceHomology
Counting overlapping breakpoints between two breakpoint setscountBreakpointOverlaps
Extracts the breakpoint sequence.extractBreakpointSequence
Returns the reference sequence around the breakpoint positionextractReferenceSequence
Finding overlapping breakpoints between two breakpoint setsfindBreakpointOverlaps
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.findInsDupOverlaps
Identifies potential transitive imprecise calls that can be explained by traversing multiple breakpoints.findTransitiveCalls
Determines whether this breakend has a valid partner in this GRangeshasPartner
Determining whether the variant is a structural variantisStructural isStructural,CollapsedVCF-method isStructural,ExpandedVCF-method isStructural,VCF-method
Determining whether the variant is a symbolic allele.isSymbolic isSymbolic,CollapsedVCF-method isSymbolic,ExpandedVCF-method
Detecting nuclear mitochondria fusion events.numtDetect
GRanges representing the breakend coordinates of structural variants #@export Partner breakend for each breakend.partner
Detecting retrotranscript insertion in nuclear genomes.rtDetect
Length of event if interpreted as an isolated breakpoint.simpleEventLength
Type of simplest explanation of event. Possible types are: | Type | Description | | BND | Single breakend | | CTX | Interchromosomal translocation | | INV | Inversion. | | DUP | Tandem duplication | | INS | Insertion | | DEL | Deletion |simpleEventType
StructuralVariantAnnotation: a package for SV annotationStructuralVariantAnnotation