Bioconductor Devel 3.15

NUMT detection from structural variant calls

Bioconductor Devel 3.15

svaNUMT identifies non-reference NUMTs by breakpoints involving one breakend on the mitochondrial genome, known NUMTs (e.g. numtS track from UCSC) and insertion sequences.

Bioconductor Devel 3.14

NUMT detection from structural variant calls

Bioconductor version: Development (3.14)

svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.