StructuralVariantAnnotation contains useful helper functions for reading and interpreting structural variants calls. The packages contains functions for parsing VCFs from a number of popular caller as well as functions for dealing with breakpoints involving two separate genomic loci. The package takes a 'GRanges' based breakend-centric approach.
* Parse VCF objects with the 'breakpointRanges()' and 'breakendRanges()'functions. * Find breakpoint overlaps with the 'findBreakpointOverlaps()' and 'countBreakpointOverlaps()' functions. * Generate BEDPE files for circos plot with 'breakpointgr2pairs()' function. * ...
For more details on the features of StructuralVariantAnnotation, read the vignette: 'browseVignettes(package = "StructuralVariantAnnotation")'
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