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Whilst both the duplication and insertion representations result in the same sequence, this representational difference is problematic when comparing variant call sets.", "topics": [ "findInsDupOverlaps" ] }, { "page": "findTransitiveCalls", "title": "Identifies potential transitive imprecise calls that can be explained by traversing multiple breakpoints.", "topics": [ "findTransitiveCalls" ] }, { "page": "hasPartner", "title": "Determines whether this breakend has a valid partner in this GRanges", "topics": [ "hasPartner" ] }, { "page": "isStructural", "title": "Determining whether the variant is a structural variant", "topics": [ "isStructural", "isStructural,CollapsedVCF-method", "isStructural,ExpandedVCF-method", "isStructural,VCF-method" ] }, { "page": "isSymbolic", "title": "Determining whether the variant is a symbolic allele.", "topics": [ "isSymbolic", "isSymbolic,CollapsedVCF-method", "isSymbolic,ExpandedVCF-method" ] }, { "page": "numtDetect", "title": "Detecting nuclear mitochondria fusion events.", "topics": [ "numtDetect" ] }, { "page": "partner", "title": "GRanges representing the breakend coordinates of structural variants #@export Partner breakend for each breakend.", "topics": [ "partner" ] }, { "page": "rtDetect", "title": "Detecting retrotranscript insertion in nuclear genomes.", "topics": [ "rtDetect" ] }, { "page": "simpleEventLength", "title": "Length of event if interpreted as an isolated breakpoint.", "topics": [ "simpleEventLength" ] }, { "page": "simpleEventType", "title": "Type of simplest explanation of event. 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