svaNUMT

svaNUMT detects NUMT events from structural variant calls by identifying nuclear-mitochondrial breakend junctions in GRanges breakend notation.

Key Features:

• NUMT detection: Identifies NUMTs by analyzing nuclear-mitochondrial breakend junctions from structural variant calls.
• Insertion site validation: Reports candidate NUMTs when a pair of valid insertion sites are found on the nuclear genome within a specified distance threshold.
• Event-based reporting: Candidate NUMTs are reported by events rather than individual breakends.

Scientific Applications:

• Nuclear-mitochondrial DNA transfer analysis: Detects NUMT (nuclear mitochondrial DNA segment) insertion events from structural variation data.

Methodology:

The tool takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. Candidate NUMTs are reported when a pair of valid insertion sites are found on the nuclear genome within a certain distance threshold.