# Variant annotations for structural variants

## Documentation for package ‘StructuralVariantAnnotation’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.breakpointRanges | Extracting the structural variants as a GRanges.
align_breakpoints | Adjusting the nominal position of a pair of partnered breakpoint.
breakendRanges | Extracting unpartnered breakend structural variants as a GRanges
breakendRanges-method | Extracting unpartnered breakend structural variants as a GRanges
breakpointgr2bedpe | Converting breakpoint GRanges to BEDPE-like dataframe
breakpointgr2pairs | Converts a breakpoint GRanges object to a Pairs object
breakpointGRangesToVCF | Converts the given breakpoint GRanges object to VCF format in breakend notation.
breakpointRanges | Extracting the structural variants as a GRanges.
breakpointRanges-method | Extracting the structural variants as a GRanges.
calculateReferenceHomology | Calculates the length of inexact homology between the breakpoint sequence and the reference
countBreakpointOverlaps | Counting overlapping breakpoints between two breakpoint sets
extractBreakpointSequence | Extracts the breakpoint sequence.
extractReferenceSequence | Returns the reference sequence around the breakpoint position
findBreakpointOverlaps | Finding overlapping breakpoints between two breakpoint sets
findInsDupOverlaps | 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.
findTransitiveCalls | Identifies potential transitive imprecise calls that can be explained by traversing multiple breakpoints.
hasPartner | Determines whether this breakend has a valid partner in this GRanges
isStructural | Determining whether the variant is a structural variant
isStructural-method | Determining whether the variant is a structural variant
isSymbolic | Determining whether the variant is a symbolic allele.
isSymbolic-method | Determining whether the variant is a symbolic allele.
numtDetect | Detecting nuclear mitochondria fusion events.
pairs2breakpointgr | Converts a breakpoint GRanges object to a Pairs object
partner | GRanges representing the breakend coordinates of structural variants #@export Partner breakend for each breakend.
rtDetect | Detecting retrotranscript insertion in nuclear genomes.
simpleEventLength | Length of event if interpreted as an isolated breakpoint.
simpleEventType | 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 |
StructuralVariantAnnotation | StructuralVariantAnnotation: a package for SV annotation