Package: StructuralVariantAnnotation 1.29.0

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]

# Install 'StructuralVariantAnnotation' in R:

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

On BioConductor:StructuralVariantAnnotation-1.29.0(bioc 3.24)StructuralVariantAnnotation-1.28.0(bioc 3.23)

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

dataimport sequencing annotation genetics variantannotation

6.40 score 2 packages 208 scripts 2 mentions 20 exports 82 dependencies

Last updated from:aaa2e0945f. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	315
linux-devel-x86_64	OK	662
source / vignettes	OK	408
linux-release-x86_64	OK	613
macos-release-arm64	OK	350
macos-oldrel-arm64	OK	292
windows-devel	OK	492
windows-release	OK	541
windows-oldrel	OK	472
wasm-release	OK	309

Exports:breakendRanges breakpointgr2bedpe breakpointgr2pairs breakpointRanges calculateReferenceHomology countBreakpointOverlaps extractBreakpointSequence extractReferenceSequence findBreakpointOverlaps findInsDupOverlaps findTransitiveCalls hasPartner isStructural isSymbolic numtDetect pairs2breakpointgr partner rtDetect simpleEventLength simpleEventType

Dependencies:abind AnnotationDbi askpass assertthat BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray dplyr fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png pwalign R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML XVector yaml

StructuralVariantAnnotation Quick Overview

Rendered fromvignettes.Rmdusingknitr::rmarkdown

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

Help page	Topics
Adjusting the nominal position of a pair of partnered breakpoint.	align_breakpoints
Extracting unpartnered breakend structural variants as a GRanges	breakendRanges breakendRanges,VCF-method
Converting breakpoint GRanges to BEDPE-like dataframe	breakpointgr2bedpe
Converts a breakpoint GRanges object to a Pairs object	breakpointgr2pairs 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 reference	calculateReferenceHomology
Counting overlapping breakpoints between two breakpoint sets	countBreakpointOverlaps
Extracts the breakpoint sequence.	extractBreakpointSequence
Returns the reference sequence around the breakpoint position	extractReferenceSequence
Finding overlapping breakpoints between two breakpoint sets	findBreakpointOverlaps
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 GRanges	hasPartner
Determining whether the variant is a structural variant	isStructural 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 annotation	StructuralVariantAnnotation

Package: StructuralVariantAnnotation 1.29.0

StructuralVariantAnnotation: Variant annotations for structural variants

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